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Revision 1.1751 - (hide annotations) (download)
Thu Oct 18 14:13:46 2012 UTC (11 years, 7 months ago) by jmc
Branch: MAIN
Changes since 1.1750: +10 -3 lines
document pkg/layers changes.

1 jmc 1.1751 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1750 2012/10/18 10:07:06 mlosch Exp $
2 jmc 1.475 $Name: $
3 cnh 1.1
4     Notes on tags used in MITgcmUV
5     ==============================
6 jmc 1.1601
7 jmc 1.1751 o pkg/layers (adjust changes from Sept 19):
8     - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
9     - snap-shot extended to all type of layers (not just the 1rst type);
10     - remove layers variables when corresponding CPP option is undef.
11     o pkg/layers:
12     - rename pkg/layers variable and add new output (layer exist & un-weighted
13     velocity in layer)
14     o pkg/seaice:
15 mlosch 1.1750 - simplify (?) ocean-drag coefficent computations by using
16     the same routine in all three solvers (saves some code lines)
17     - remove global fields DRAGA and DRAGS from C-grid code and
18     declare them locally in lsr.F (the only place where they are
19     still used)
20 mlosch 1.1749 o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
21     (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
22     and SEAICEuseJFNK=.true. A few things to note:
23     - involves a FGMRES, that is parallel but very inefficient,
24     because of many scalar products (global sums) in the Gram-Schmidt
25     orthogonalization method. Needs to be replaced. Original code
26     from J.-F. Lemieux
27     - preconditioner for FGMRES is a stripped down version of LSOR
28 jmc 1.1751 - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
29 mlosch 1.1749 preconditioner. For the preconditioner, the default is set to 10.
30     - Jacobian times vector is computed with finite differences
31     - marginally related to JFNK-solver: add a smooth regularization for
32     zeta with tanh that will improve convergence (Lemieux and Tremblay,
33     2009) for any implicit solver (not implemented for EVP because EVP
34     does not need this regularization in the first place). Define
35     SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
36 jmc 1.1748 o eesupp/src:
37     - check in genmake2 that intrinsic S/R flush is available.
38     - add S/R to flush IO unit (if intrinsic S/R flush is available)
39     - flush standard & error msg unit before MPI termination
40     - if debugMode, flush IO unit after printing msg
41     o pkg/ctrl:
42     - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
43     to ctrl_set_unpack_xyz.
44    
45 jmc 1.1747 checkpoint64 (2012/10/09)
46 heimbach 1.1745 o pkg/shelfice
47 jmc 1.1747 - in mom_fluxform.F, mom_vecinv.F:
48     CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
49     Bug fix KappaRU -> KappaRV
50     does not change verification/isomip but may change other setups
51     (presumably constant KappaRU=KappaRV)
52 mlosch 1.1746 - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
53 dimitri 1.1744 o pkg/obcs:
54     - fixed some indexing bugs in obcs_seaice_sponge.F
55     - added obcs relaxation subroutines for HSALT and HSNOW
56     - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
57 mlosch 1.1743 o pkg/seaice:
58     - add "multicategory" parameterization for snow in analogy to ice,
59     default is off for now.
60 jmc 1.1741 o pkg/obcs:
61 dimitri 1.1742 - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
62     see verification/seaice_obcs/input.seaiceSponge for example application.
63 jmc 1.1741 - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
64     index setting by master-thread. This fix multi-threads Pb in previous modifs.
65 gforget 1.1740 o pkg/layers :
66 jmc 1.1741 - add diagnostics to pkg/layers
67     - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
68     (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
69 gforget 1.1740 o pkg/generic_advdiff/gad_implicit_r.F :
70 jmc 1.1741 - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
71     o pkg/seaice/seaice_growth.F:
72 gforget 1.1740 - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
73 jmc 1.1738 o pkg/obcs:
74 jmc 1.1739 - change default setting of OBCS_UVICE_OLD from defined to undef;
75     - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
76     in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
77     - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
78     - change OB null index value (OB_indexNone) to -99 ; this fix the problem
79     with Southern & Western OB at a tile edge (at least in a simple set-up).
80     o pkg/obcs:
81 jmc 1.1738 - change settings of OB index in case OB coincides with tile edge (shared by
82     2 tiles), so that common OB location is registered by both tiles (instead of
83     only 1). However, for Southern and Western OB, index value = 0 is not
84     recognized as valid OB index (=default null value) and needs to be fixed.
85     - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
86 jmc 1.1739 - new parameter "OB_indexNone" for null index value (for now, still zero)
87 jmc 1.1738 to replace hard-coded null index value of zero.
88 jmc 1.1737 o pkg/exch2:
89     - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
90     always check buffer-size (but outside the loop); move checking for valid
91     index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
92     print each tile and point connection only if |W2_printMsg|>= 2 and 3.
93 jmc 1.1736 o pkg/ctrl (pack & unpack):
94     - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
95     (locally defined) for different variables (+ remove the variable-specific
96     file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
97     (to be extended to other local file names in ctrl.h).
98     o pkg/flt:
99     - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
100 jmc 1.1735 o pkg/mdsio:
101     - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
102 jmc 1.1734 o tools/genmake2:
103     - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
104     (added by Alistair in version 1.51 for building without make depend);
105     - remove Header files list (H_SRC_FILES) from the dependence of targets
106     ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
107     place in version 1.23): this save going through staf when unrelated header
108     file has been modified.
109     Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
110     "make depend" step, still need to do "make links" before "make adtaf".
111 jmc 1.1733 o eesupp/src (+ few pkg src files) & genmake2:
112     - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
113     - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
114 jmc 1.1734 - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
115 jmc 1.1733 upper/lower case ; account for space between "#" and undef/define)
116     o pkg/flt (with exch2):
117     - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
118 jmc 1.1734 - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
119 jmc 1.1733
120 jmc 1.1730 checkpoint63s (2012/09/05)
121 gforget 1.1731 o pkg/ecco:
122 jmc 1.1732 - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
123     - add more relevant #ifdef ALLOW_SMOOTH ones.
124     - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
125 gforget 1.1731 o pkg/ctrl:
126     - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
127     ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
128 jmc 1.1732 - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
129     doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
130     ctrlSmoothCorrel3D (new).
131 gforget 1.1731 The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
132     - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
133 jmc 1.1732 - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
134 gforget 1.1731 controls when useAtmWind, and vice versa.
135     - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
136     - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
137 jmc 1.1732 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
138     - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
139     #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
140     - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
141     replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
142 gforget 1.1731 o pkg/smooth:
143 jmc 1.1732 - remove un-necessary includes.
144     - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
145     Those CPP options were never defined, and not necessary.
146 gforget 1.1731 o model/src:
147     - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
148     - standard treatment of useSMOOTH.
149     o pkg/autodiff:
150 jmc 1.1732 - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
151     useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
152 jmc 1.1729 o pkg/exch2:
153     - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
154 gforget 1.1731 + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
155 jmc 1.1729 - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
156     and tiles to process mapping.
157     - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
158     moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
159     rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
160     from w2_eeboot.F to w2_readparms.F.
161     o eesupp/src:
162     - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
163     ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
164     also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
165     - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
166     is defined (remove condition on usingMPI) to match cases where MPI_INIT
167     has been called.
168     - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
169     - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
170     (so that on 1 proc, get same myPid independently of usingMPI)
171     - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
172     useCubedSphereExchange with EXCH-1 (safer).
173     - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
174 jmc 1.1728 o pkg/ggl90:
175     - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
176     used in ALLOW_GGL90_SMOOTH code.
177     o pkg/flt:
178     - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
179     floats at the Southern end of the domain).
180     o eesupp/inc:
181     - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
182     but not used (and not to be used) anywhere, just for documentation.
183 jmc 1.1727 o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
184     - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
185     a) can damage previously written records in any other multi-record files.
186     b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
187 jmc 1.1726 o tools/genmake2:
188     - define variable MAKE within Makefile and use it in place of 'make';
189     - update AD_CONFIG.h (if needed) before building any of the executable
190     (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
191     and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
192     - always print usual warning comment 'this file is automatically generated'
193     from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
194 jmc 1.1727 o pkg/cheapaml:
195     - updated to correspond to the code used in accepted paper (Nico Wienders).
196 jmc 1.1726 o pkg/exf:
197     added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
198     ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
199     and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
200     o pkg/exf, autodiff, ctrl, ecco and seaice:
201     remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
202     o pkg/ctrl, ecco:
203     allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
204     Depending on useAtmWind, one is inactive, and the other is active (see
205     exf_getffields.F/exf_getsurfacefluxes.F).
206 jmc 1.1724 o tools/genmake2:
207     - improve error msg when failing in 2nd test of check_for_broken_Ff
208     - fix option '-makefile' short-name (-mf according to genmake2 -help)
209     - source local config file "genmake_local" just after processing the genmake2
210     command arguments (previously done before processing arg).
211 jmc 1.1723 o pkg/grdchk:
212     - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
213     to this routine from cost_final has been dropped in g_cost_final)
214     - improve printed information (more explicit msg, no longer using "print *,"
215     fix fcpertminus printed value).
216 jmc 1.1722 o model/src:
217     - move call to COST_INIT_VARIA out of packages_init_variables.F directly
218     into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
219     this prevents getting cost-funct reset in adinitialise_varia recomputations.
220 jmc 1.1721 o pkg/dic:
221     - move initialisation of "freefe" array from from dic_biotic_forcing.F to
222     fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
223     o pkg/grdchk:
224 gforget 1.1720 - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
225 jmc 1.1721 - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
226 gforget 1.1719 o pkg/autodiff/ctrl/grdchk :
227 jmc 1.1721 - attempt to sort out what works and what does not,
228 gforget 1.1719 with regard to I/O, and to warn/stop accordingly.
229 jmc 1.1721 o pkg/grdchk:
230 gforget 1.1719 - attempt to fix grdchk in the case of useSingleCpuIO.
231     - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
232     statements were moved from grdchk_main.F and into
233     grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
234     - a global sum is applied to record numbers icvrec/layer
235     out of grdchk_loc so that they be passed to I/O routines.
236 jmc 1.1721 o pkg/smooth:
237     - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
238 gforget 1.1719 smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
239 jmc 1.1717 o verification/testreport:
240     - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
241     - can also use compressed (gzip) reference output file;
242     - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
243     to be easier to collect by testreport.
244     - update existing TLM output (half out-of-date by more than 3 yrs).
245 jmc 1.1718 - report NETCDF & LAPACK settings (from genmake2) in output dir.
246     - report run-time in each individual summary (previously only for AD test);
247     for TLM test, add also TAF version.
248     - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
249 jmc 1.1717
250 jmc 1.1716 checkpoint63r (2012/08/15)
251     o tools/genmake2:
252     - fix Makefile for target ftlall (+ update files to clean after make ftlall)
253 gforget 1.1715 o pkg/ecco/ecco_cost_final.F :
254 jmc 1.1716 - fix fc print statements (to stdout and costfunction0000) so
255 gforget 1.1715 that the printed value is always after the global sum.
256     o pkg/seaice/seaice_dynsolver.F :
257     - fix ice strength assymptote at SEAICE_area_max<1
258     (no change for the standard case of SEAICE_area_max=1)
259 jmc 1.1714 o some cleaning:
260 jmc 1.1716 - pkg source files: ensure that all *.F files from each pkg included the
261 jmc 1.1714 corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
262 jmc 1.1716 only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
263 jmc 1.1714 code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
264 jmc 1.1716 includes;
265 jmc 1.1714 - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
266 jmc 1.1716 - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
267     is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
268 jmc 1.1714 ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
269     - update option-file CPP_OPTIONS.h of all AD experiments:
270 jmc 1.1716 * no longer include PACKAGES_CONFIG.h ;
271     * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
272     * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
273 jmc 1.1714 including ECCO_CPPOPTIONS.h).
274 jmc 1.1713 o pkg/cost, pkg/ctrl, pkg/ecco option-file:
275     - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
276     separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
277     not necessary accurate).
278     - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
279     pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
280     deliberately break compilation (a remainder that it needs to be customized)
281     - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
282     - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
283     - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
284     o tools/genamke2:
285     - check for lapack.
286 gforget 1.1712 o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
287 jmc 1.1713 - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
288     jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
289     from both packages.
290 gforget 1.1712 - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
291     - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
292 jmc 1.1713 - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
293     of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
294 gforget 1.1712 o pkg/cost : add comments to explain special and/or untested setups.
295 jmc 1.1711 o pkg/exf:
296     - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
297     (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
298     o verification/*/code_ad:
299     mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
300     - reccord when this file is included (define ECCO_CPPOPTIONS_H)
301     - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
302     allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
303 gforget 1.1710 o pkg/seaice :
304 jmc 1.1711 - added possibility to change ice strength/PRESS0 relationship to
305     HEFF, according to the following run time parameters
306     SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
307     SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
308     SEAICEpresH0 :: HEFF threshold for ice strength (m)
309 gforget 1.1710 o pkg/ggl90 :
310 jmc 1.1711 - added run time flag mxlSurfFlag to include the code that ensure
311 gforget 1.1710 mixing between first and second level (previously included as a comment)
312 gforget 1.1709 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
313 jmc 1.1711 - add test of newly added dumpAdByRec=T option where
314 gforget 1.1709 we write all records to one file per variable.
315     o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
316     - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
317     to check that this code is ok with taf and compiles in adjoint.
318     o pkg/autodiff :
319     - added run time param dumpAdByRec : ad dump format switch.
320 jmc 1.1711 If true then write all records to one file per variable.
321     Else write one file per record (remains the default).
322 gforget 1.1709 - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
323 gforget 1.1708 o pkg/seaice:
324     - Added SEAICEuseTILT run time switch : if set to
325 jmc 1.1711 false then omit the tilt term in seaice dynamics.
326 gforget 1.1708 - Fix free drift calculation.
327 heimbach 1.1707 o pkg/shelfice:
328 jmc 1.1711 When initializing SHELFICEDragQuadratic, set default to be
329     consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
330 heimbach 1.1707 but retain option to set it independently
331     (inconsistenty spotted by Veronique Dansereau)
332 jmc 1.1706 o eesupp/inc:
333     - in EEPARAMS.h, add real-type constant for some frequently used simple number
334     (0,1,2,1/2), with name explicitly referring to RS/RL type.
335     o model/src:
336     - move balancing of relaxation terms to new S/R balance_relax.F.
337 jmc 1.1702 o pkg/autodiff:
338     re-write active I/O high-level (control) S/R:
339     - rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
340     - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
341     - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and
342     MDS_READ/WRITE_FIELD); change loops to multi-threads.
343     - update and merge active_file_control_slice.flow into active_file_control.flow
344     - update the calls in lower level S/R (active_file.F, active_file_g.F and
345     active_file_ad.F) keeping the argument list and function unchanged.
346 jmc 1.1703 - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
347     =.TRUE.") and remove high-level (control) _loc version (not called anymore).
348 jmc 1.1704 - new low-level active I/O routines, one for each type (RL/RS), for active var
349     of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
350     fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
351     right type.
352 jmc 1.1702 o autodiff and RS=real*4:
353     - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
354     ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
355     - change argument type of 3-D mask argument to _RS to match type in the call
356     (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
357 jmc 1.1701 o pkg/thsice:
358     - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
359     - option to correct ocean fresh-water flux for imbalance of Atmos+Land
360     fresh-water flux: uniform correction or proportional to local precip.
361 heimbach 1.1700 o pkg/ctrl:
362     - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
363     - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
364     ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
365     - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
366 jmc 1.1701
367 jmc 1.1699 checkpoint63q (2012/07/30)
368 jmc 1.1697 o pkg/autodiff:
369     note about monitor and snap-shot of ad-variables:
370     a) need to apply ADEXCH before monitor or output of ad-vars to include
371     overlap contributions (was done for adjDump but missing for monitor).
372     b) since ADEXCH implies adding overlap values to interior array, machine
373     truncation error is expected when adding an ADEXCH call in the middle of
374     the time-stepping (although mathematically identical).
375     modifs:
376 jmc 1.1698 - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
377     declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
378 jmc 1.1697 - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to
379     apply ADEXCH before monitor or snap-shot of ad-variables:
380     =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
381     - implement new method (copy+adexch) for snap-shot and monitor of main model
382 jmc 1.1698 ad-vars (initially not used by default -> output unchanged).
383     - change default (set to 2) to use new method and update few output_adm.txt
384     with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
385     and both tutorial_tracer_adjsens tests).
386     - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
387     and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
388 heimbach 1.1696 o pkg/ctrl:
389     enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
390     generic control variables via
391     #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
392     Only required customization should be S/R ctrl_map_ini_genarr.F
393     (routine in repository contains example)
394 jmc 1.1695 o pkg/exf:
395     - fix and refine checking of surface-relaxation setting when using EXF
396 jmc 1.1694 o verification (adjoint exp):
397     - reduce length of simulation by half for experiment global_ocean.cs32x15
398     (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
399 mlosch 1.1693 o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
400 jmc 1.1694 - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
401 mlosch 1.1693 of KE that can occur with aggressive optimization
402 jmc 1.1694 + put quadratic bottom drag calculation in separated loops (only done if
403     using bottomDragQuadratic)
404 jmc 1.1692 o model/src: CG2D_NSA
405     - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF
406     and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
407     - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
408     change cg2d residual target to be expressed in Wunits (=> do not normalise
409     RHS ; this fix global_max Pb with TAF); update output.
410 jmc 1.1691 o verification/tutorial_tracer_adjsens:
411 jmc 1.1692 improve parameter consistency (and get rid of warnings):
412 jmc 1.1691 - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
413     - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
414     - use staggerTimeStep (for stability) in som81; use default rotation period.
415 jmc 1.1690 o pkg/exch2:
416     - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
417     reset to 0 = 1 long line in X)
418     o pkg/mdsio:
419     - fix reading of dimensions from meta file for large-size domain
420 jmc 1.1689 o model/src:
421     - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
422     - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
423     Cubed-Sphere Exch with CS-corners inside the domain;
424     make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
425     globalArea and to set hasWetCSCorners.
426     - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
427     metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
428     - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
429     useCDscheme and useCubedSphereExchange).
430 gforget 1.1688 o pkg/seaice/seaice_growth.F :
431 jmc 1.1689 - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
432     for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
433     when the previous code was not correct.
434     - in all cases diagnoze the boundary condition mismatch to SIaaflux
435     - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
436     that term to QNET (essentially to set the melt/freeze water to 0degC).
437     when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
438 gforget 1.1687 o verification/global_ocean.cs32x15/input.seaice :
439 jmc 1.1689 - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
440     - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
441     - update results (output.seaice.txt) accordingly.
442 gforget 1.1687 o verification/lab_sea/input/data.seaice :
443 jmc 1.1689 - remove SEAICEheatConsFix, which is now be tested
444     in global_ocean.cs32x15. The presently coded fix
445     is only consistent with real fresh water + nlfs.
446     - update results (output.txt) accordingly.
447 gforget 1.1686 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
448 jmc 1.1685 o AD_CONFIG.h file:
449 jmc 1.1689 - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
450     - remove #include "AD_CONFIG.h" from all included OPTIONS files and
451     add it explicitly in each fortran src file where it is needed.
452     motivation: header file AD_CONFIG.h is generated/modified after "make depend"
453     thus introducing potentially wrong dependency; therefore, better to include
454     it only where it's really needed, and after any other included OPTIONS file
455     (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
456     or ALLOW_TANGENTLINEAR_RUN).
457 jmc 1.1685
458 jmc 1.1684 checkpoint63p (2012/07/06)
459 jmc 1.1681 o pkg/autodiff:
460     - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
461     - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
462     which are now read from new parameter file "data.autodiff" (inAdExact
463     previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
464     - add file "data.autodiff" in all verification/*/input_ad/ directories.
465 jmc 1.1682 - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
466     mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
467 heimbach 1.1680 o verification/tutorial_tracer_adjsens/
468     - add extra sub-verification which uses "SOM" advection scheme
469     (2nd Order-Moment Advection Scheme, Prather Limiter) with
470 jmc 1.1681 #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
471 heimbach 1.1680 and in data:
472 jmc 1.1681 multiDimAdvection=.TRUE.,
473     tempAdvScheme=81,
474     saltAdvScheme=81,
475 gforget 1.1683 o model/src:
476     - introduce ALLOW_BALANCE_RELAX which allow the removal
477     of the global mean of relaxation terms by setting
478     balanceThetaClimRelax and balanceSaltClimRelax
479 jmc 1.1684 - disable balanceEmPmR and balanceQnet in the case when useSeaice.
480 gforget 1.1683 This case is now treated appropriately in seaice_growth.F
481     o pkg/seaice:
482 jmc 1.1684 - do balanceEmPmR and balanceQnet based on the net fluxes
483     (SItflux) that enter the ocean+ice system rather than QNET
484     and EMPMR. Works best in real fresh water.
485     - SIatmFW, SIatmQnet, and SItflux computations had to be moved
486     out of the diagnotics bloc, and stored in global arrays.
487 heimbach 1.1680
488 jmc 1.1679 checkpoint63o (2012/06/29)
489 jmc 1.1678 o vertical mixing schemes:
490     - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
491     - replace computation of density (in Function STATE1, opps_calc.F) by a call
492     to S/R FIND_RHO_SCALAR
493     - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
494     and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
495     affects output (vermix.ggl90) at truncation level.
496 jmc 1.1677 o testreport:
497     - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
498     (nSx,nSy) for the number of threads (from eedata.mth)
499 jmc 1.1676 o model/src:
500     - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
501     related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
502 heimbach 1.1675 o verification/tutorial_tracer_adjsens/
503     - compile with ALLOW_CG2D_NSA
504     - run with nonlinFreeSurf=3
505     - update reference output_adm.txt
506 jmc 1.1674 o tools/genmake2:
507     - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
508     refine usePROFILES switching off (only when NetCDF is not available).
509 jmc 1.1673 o verification (atmospheric set-up):
510     - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
511 gforget 1.1672 o pkg/profiles : refine profiles and files handling.
512     o model/src and pkg/ecco : introduce run-time switch usePROFILES.
513 gforget 1.1671 o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
514     - changes to use model/src/the_main_loop.F rather than the ecco version
515     in ecco type adjoint runs.
516 jmc 1.1670 o model/src:
517 jmc 1.1673 - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
518     - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
519     - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
520     o model/src:
521     - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
522 jmc 1.1670 update output of test experiment bottom_ctrl_5x5.
523 jmc 1.1669 o pkg/generic_advdiff:
524     - implement vertical bi-harmonic diffusion (for now, only for T & S and
525     only explicitly).
526 heimbach 1.1668 o verification/bottom_ctrl_5x5/
527     update reference output (results changed quite some time ago,
528     not sure when; but new reference results look ok in terms of grdchk)
529 heimbach 1.1667 o verification/1D_ocean_ice_column/
530     For verification purposes, the exact adjoint rather than an approx.
531     should be used (e.g., to comare against F.D. or TLM).
532     removed autodiff_inadmode*_ad.F routines in code_ad/
533     Update results/ accordingly.
534 jmc 1.1666 o pkg/cal:
535     - change cal_getdate.F so that output date is function of input time only
536     (less ambiguous, not mixed up with input iteration number).
537     - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
538 jmc 1.1665 o pkg/diagnostics:
539     - implement calendarDumps also for stats-diags
540     - implement calendarDumps also for snap-shot output (negative freq)
541     - for now, ignores calendarDumps if non-zero phase-lag.
542    
543 jmc 1.1664 checkpoint63n (2012/06/04)
544 jmc 1.1662 o model/src:
545     - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
546     between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
547 jmc 1.1663 - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
548     similar to calc_r_star.F); update results of experiment internal_wave and
549 jmc 1.1662 tutorial_global_oce_in_p (affected @ truncation level).
550     o pkg/shelfice:
551     - add parameterisation of advective-diffusive flux into the ice shelf
552 mlosch 1.1661 according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
553     - simply eps3/3a computation
554 jmc 1.1660 o eesupp:
555     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
556     between tiles, just fill-in edges assuming locally periodic subdomain) and
557     add corresponding exchange subroutines (EXCH0);
558     - new CG-solver version (_EX0) for disconnected-tiles special case.
559 jmc 1.1659 o model/src (CG-solvers):
560     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
561     (similar final residual output and max-Iter number as with standard version);
562     - allows to store and use lowest-residual solution (standard & _SR versions);
563     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
564     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
565     o eesup/src:
566     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
567     ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
568 heimbach 1.1658 o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
569    
570 jmc 1.1657 checkpoint63m (2012/04/27)
571 jmc 1.1656 o pkg/shelfice:
572     - account for partical cells in surface level below ice-shelf for hydrostatic
573     pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
574 jmc 1.1654 o ad test experiments:
575     - update and rename to "ad_optfile.local" local AD-optfile specific to a
576     particular adjoint verification experiment (in verification/*/code_ad/)
577 heimbach 1.1653 o pkg/seaice & pkg/exf:
578 jmc 1.1654 - Part two of ECCO-CLIVAR code merges.
579 heimbach 1.1653 Completes merge of seaice area relax. code.
580     Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
581     to be set in EXF_OPTIONS.h since this pkg controls its I/O
582     (and avoids second CPP option in SEAICE_OPTIONS.h)
583 jmc 1.1654 - change default value of costIceStart & costIceEnd to a valid date.
584 dimitri 1.1655 - add snowPrecip to HSNOW in seaice_growth
585 jmc 1.1652 o pkg/ptracers:
586     - move ptracers summary and setup check into separated S/R ; add a check for
587     valid PTRACERS_Iter0 value (error+stop or just warning).
588 jmc 1.1651 o pkg/cal (+ pkg/ecco):
589     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
590     as input; and for AD, unless both are not differentiable (e.g., k index)).
591 jmc 1.1650 o model/src:
592     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
593     is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
594     temporary set to usingZCoords value (to be changed to F when using shelfice).
595     - hydrostatic pressure: implement partial cell near the surface also for
596     Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
597     usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
598     o pkg/ctrl/ctrl_init.F:
599     - add a formal parameter to s/r ctrl_init_rec to print
600 mlosch 1.1649 xx_$(ctrl_valiable)_file for easier debugging
601     - move call of cal_* routines into the if-block where they are really
602 jmc 1.1650 needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
603 mlosch 1.1649 to specify a startdate
604 jmc 1.1648 o pkg/seaice:
605     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
606     global_ocean.cs32x15/code versions).
607     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
608     verification experiment global_ocean.cs32x15.seaice and update results.
609 jmc 1.1647 o pkg/exf:
610     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
611     (according to useExfYearlyFields).
612 jmc 1.1646 o pkg/cal:
613     - move calendar setting & summary (previously in cal_readparams.F) into new
614     S/R CAL_INIT_FIXED to be called later in the initialisation process, once
615     length of the simulation is set (after SET_PARMS call); This is an attempt
616     to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
617     - For safety: keep a record of pkg/cal parameter settings status
618     to allow to STOP if one pkg/cal S/R is called too early.
619 jmc 1.1647 - add a stop in all basic pkg/cal subroutines if called before setting is done.
620     - modify cal_getdate.F: stop when nothing was returned;
621     if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
622     this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
623 jmc 1.1646
624 jmc 1.1645 checkpoint63l (2012/04/04)
625 jmc 1.1644 o pkg/bbl:
626     - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
627     update global_with_exf output.yearly.txt file.
628 jmc 1.1643 o pkg/cal:
629     - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
630     - remove 2 unsused and very short (1 line only) functions ;
631     - remove unsused subroutines from AD-Diff list.
632 jmc 1.1642 o model/src:
633     - start to implement clean wait to stop in initialization S/R (config_check.F,
634 jmc 1.1645 packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
635 jmc 1.1642 o folowing PRINT_MESSAGE changes:
636     - remove reminder multiple print to the same file (STDOUT) when multi-threads.
637 dimitri 1.1641 o pkg/bbl:
638     - modification so it can work with z*
639     - replace deltaT with dTtracerLev(k) for asynchronous time stepping
640     - global_with_exf/input.yearly verification; changes output.yearly.txt
641 jmc 1.1639 o eesupp/src:
642     - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
643     writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
644     - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
645     # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
646     - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
647     - when using MPI, always set usingMPI=T ; set default accordingly and stop
648     if not consistent.
649     - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
650     argument is zero (in case called within single-thread section).
651 jmc 1.1638 o pkg/fizhi:
652     clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
653     in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
654 jmc 1.1637 o pkg/exch2:
655     - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
656     activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
657     - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
658     but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
659     with bad ones coming from a not-yet-updated halo.
660     This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
661 dimitri 1.1636 o pkg/frazil:
662 jmc 1.1637 move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
663     http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
664 mlosch 1.1635 o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
665 heimbach 1.1634 o verification/lab_sea
666     * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
667     * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
668     * nTimeSteps 3 -> 4
669     * changed reference output accordingly
670     o pkg/ctrl:
671     * fix ctrl_get_gen for xx_sst, xx_sss
672 jmc 1.1632 o pkg/fizhi:
673     - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
674     update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
675 jmc 1.1633 - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
676     fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
677     clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
678 jmc 1.1631 o pkg/gmredi:
679     - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
680 jmc 1.1630 o pkg/fizhi:
681     - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
682     (old)aces open64 tuv test.
683 dimitri 1.1628 o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
684 jmc 1.1629 o pkg/mom_vecinv:
685     - fix 1 loop range in mom_vecinv.F to be like all the other loops which
686     set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
687     with non-lin free-surf).
688     o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
689     in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
690 mlosch 1.1627 some compilers (gfortran 4.6.0 on MacOS)
691 jmc 1.1626 o momentum:
692     - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
693     & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
694     fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
695    
696 jmc 1.1625 checkpoint63k (2012/03/17)
697 jmc 1.1624 o model/src:
698     - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
699     flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
700     - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
701     (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
702 jmc 1.1622 o model/src: solve_*diagonal.F
703     - replace division with multiplication by inverse (similar to original version)
704 jmc 1.1623 update output of AD exp. global_ocean.90x40x15.
705 jmc 1.1622 - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
706     to enable the use of the vectorized & differentiable solve_tridiagonal.F
707 jmc 1.1623 - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
708     vertical advection (to get solve_tridiagonal tested in AD mode).
709 jmc 1.1622 o pkg/seaice: ECCO-CLIVAR merge:
710     1. seaice AREA relaxation
711 heimbach 1.1621 * CPP option: SEAICE_ALLOW_AREA_RELAXATION
712     * runtime flag: SEAICE_tauAreaObsRelax
713 jmc 1.1622 2. modified global mean cost imbalance code: CPP option
714     ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
715 heimbach 1.1620 o another iteration on solve_*diagonal.F
716 jmc 1.1622 Make choices independent of AUTODIFF
717     Default will be the adjoinable vectorized version.
718     Alternative choices are:
719     * non-adjoinable original version with low memory footprint:
720     #define SOLVE_DIAGONAL_LOWMEMORY
721     * still adjoinable but does not vectorize (k as inner-most loop):
722     #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
723 jmc 1.1619 o testreport
724     - add option to use a home made wrapper around "make"
725     - remove MITGCM_IEEE env. variable (no longer active)
726 mlosch 1.1618 o pkg/shelfice
727     - improve computation of friction velocity for velocity dependent
728     exchange coefficients: include velocities into SHELFICEBoundaryLayer
729     block to average velocities vertically
730     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
731 heimbach 1.1617 o Modify diagonal solvers, now three versions (upon request):
732     #ifndef SOLVE_DIAGONAL_AUTODIFF
733     1. default version (dating back a while ago)
734     #else /* def SOLVE_DIAGONAL_AUTODIFF */
735     # ifdef SOLVE_DIAGONAL_KINNER
736     2. adjoinable version with k-innermost loop (G. Forget)
737     # else
738     3. adjoinable vectorized version of 2.
739     # endif
740     #endif /* SOLVE_DIAGONAL_AUTODIFF */
741     All flags are currently set within routines, but could/should be moved to CPP-options.
742     Array bounds for 1. are as before, for 2.,3. cover the entire domain
743     (could be changed for 1. too).
744 jmc 1.1616 o verification/lab_sea (fwd):
745     - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
746     use 7 categories (except hb87), new solve4temp params (except salt_plume),
747     constant salinity (=4) or variable salinity (salt_plume) done through
748     SItracer.
749 jmc 1.1615 o pkg/seaice:
750     - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
751     - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
752     SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
753     from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
754     SEAICE_freeze got retired) but already better than previously with
755     SEAICE_freeze=123456.7 deg.C;
756     - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
757     (safer multi-threaded setting); always set SEAICEuseEVP;
758     - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
759     SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
760     stop if multiple specifications for the same coeff; make sure default
761     SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
762 jmc 1.1614 o pkg/obcs:
763     - allow to switch to upwind 1rst order advection scheme for the advective
764     flux computation at the open-boundary; disabled for adjoint built.
765 jmc 1.1613 o pkg/ptracers:
766     - rename PTRACERS_RESTART.h -> PTRACERS_START.h
767     - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
768     - add parameter to decide when to start a tracer; use internal flag to
769     know which tracer to step-forward; switch this internal flag at the top
770     of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
771     for adjoint built.
772 jmc 1.1612 o pkg/seaice:
773     - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
774     - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
775     - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
776 jmc 1.1611 o pkg/ecco:
777     - fix writing of output file DiagnosCost_ClimSalt/Theta
778     and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
779 jmc 1.1612 o pkg/seaice:
780 jmc 1.1610 - add missing initialisation of COR_ICE array in dynsolver.F
781     - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
782     compiled either way, and is tested in all exps (multidim was only tested
783     in lab_sea ad before).
784     - cosmetic change to prepare for future addition of ITD. no change to results.
785     no defaults change.
786 gforget 1.1609 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
787 jmc 1.1610 - by lack of adequate verification experiments, I further used custom versions
788     of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
789     should be correct.
790 gforget 1.1609 - avoid recomputations in ad.
791 jmc 1.1608 o array initialisation in adjoint mode:
792     1) pkg/mom_common/mom_calc_ke.F:
793     add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
794     The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
795     part this initialisation is gone, resulting in Floating Point Exception
796     (caught by open64 compiler with debug option).
797     2) model/src/convective_weights.F
798     set output convectCount over the full array range (instead of doing
799     an update): this fix a similar issue when called within recomputation (adjoint)
800     which could by-pass the initialisation (normally done in the caller S/R).
801     o pkg/seaice:
802 gforget 1.1604 - final version of turbulent flux params, as agreed at MIT ice meet:
803     SEAICE_mcPheePiston (default is ~ 0.000875)
804     SEAICE_mcPheeTaper (default is 0.)
805     SEAICE_frazilFrac (defualt is 1.)
806     SEAICE_mcPheeStepFunc (default is false)
807 dimitri 1.1605 - changes results at trunction error level
808     - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
809 jmc 1.1608 o added pkg/frazil:
810     - see frazil_description.tex for details
811 dimitri 1.1607 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
812 mlosch 1.1602 o pkg/shelfice/shelfice_thermodynamics.F
813 jmc 1.1608 - fix exponents for velocity dependent exchange coefficients: change
814 mlosch 1.1602 from 2/3(=0) to 0.66666666666666667
815 jmc 1.1608 - move computation of velocity dependent exchange coefficients into
816 mlosch 1.1602 separate loop, so that it applies to both thermodynamics
817     - move some divisions by constants out of loops
818    
819 jmc 1.1601 checkpoint63j (2012/02/16)
820     o pkg/seaice:
821     - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
822     - SItracer: added run time params, and allow coupling to ocn salinity.
823 jmc 1.1599 o pkg/seaice: remove (almost) all divisions by constants within loops
824     in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
825 mlosch 1.1598 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
826 jmc 1.1599 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
827     output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
828     o pkg/seaice :
829 jmc 1.1601 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
830     = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
831 gforget 1.1596 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
832 jmc 1.1599 - add permanent SItflux diag that corresponds to TFLUX but includes
833 jmc 1.1601 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
834 jmc 1.1599 - allow activation/testing of a fix for suspected missing term in
835 jmc 1.1601 ocn-ice heat budget (to be confirmed). To test this, you want to
836     undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
837     SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
838 gforget 1.1596 - no change in results, fwd or ad.
839 jmc 1.1601 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
840 jmc 1.1599 - switch to variable freezing point.
841 gforget 1.1595 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
842     - bug fix : the sublimation term that was missing is now activated.
843     Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
844 jmc 1.1599 - bug fix : flooding sign term for SIsal0.NE.0.
845 gforget 1.1595 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
846     o pkg/seaice:
847     - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
848 jmc 1.1601 is now the default, and the old default constant freezing point is recovered
849     with SEAICE_tempFrz0 = -1.96,
850     SEAICE_dTempFrz_dS = 0.,
851     - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
852 gforget 1.1595 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
853 jmc 1.1599 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
854 jmc 1.1601 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
855 jmc 1.1599 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
856 jmc 1.1601 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
857 jmc 1.1599 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
858 jmc 1.1601 seaice_growth r149 for legacy branch (no results change).
859     - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
860     from I. Fenty).
861     - results did not change except for global_ocean.cs32x15, mostly due to the
862     switch to variable freezing point (see above item for detail).
863 jmc 1.1594 o pkg/thsice:
864     - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
865     seawater freezing in thsice_calc_thickn (not used).
866 gforget 1.1593 o pkg/seaice: turbulent flux term specification via run time params.
867     - replace CPP switches with run time switches to facilitate testing
868 jmc 1.1601 - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
869     GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
870 gforget 1.1593 - added runtime parameter : SEAICEturbFluxFormula
871     - move Mcphee constants to SEAICE_PARAMS.h
872     - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
873 jmc 1.1601 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
874     remove seaice_summary call (moved to seaice_init_fixed)
875 jmc 1.1594 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
876     SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
877 jmc 1.1601 - seaice_summary.F : add missing report of read turbulent flux term set up
878     and SITRACER.
879     - seaice_check.F : check range; inform and stop if retired CPPs are used
880     (incl. SEAICE_AGE).
881 jmc 1.1594 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
882 jmc 1.1601 CPP switch, same computation as before for the different options.
883 gforget 1.1593 - change results at the truncation level.
884 jmc 1.1592 o pkg/seaice:
885     - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
886     useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
887     SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
888     - update verification/*/input*/data.seaice:
889     to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
890     code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
891     and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
892     set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
893 jmc 1.1591 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
894     - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
895     algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
896     difference in results only due to machine truncation.
897     - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
898     MaykutPolySatVap; keep MIN_LWDOWN.
899     - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
900     - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
901     + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
902 jmc 1.1590 o pkg/salt_plume:
903 jmc 1.1591 - isolate saltPlumeFlux array exch into a specific S/R called from
904     do_oceanic_phys.F
905     - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
906 jmc 1.1590 o verification:
907 jmc 1.1591 - move untested set-up to MITgcm_contrib/verification_other.
908 jmc 1.1588 o pkg/seaice:
909 gforget 1.1589 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
910     o pkg/seaice:
911 jmc 1.1588 - seaice_solve4temp.F (keeping results unchanged):
912     * add 2 future run-time params to select which saturation vapor pressure
913     formula is used and how post-iteration fluxes are set.
914     Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
915     * New piece of code (not used) to update surf. atmos. heat flux F_ia using
916     the linearized expression to stay consistent with tsurf finding.
917     - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
918     can be < 0.
919 jmc 1.1587 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
920     - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
921     conductive heat flux F_c , and add it explicitly when updating tsurf as
922     solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
923     so that now F_ia has a consistent meaning through the entire routine.
924     This causes differences at truncation level: update output of fwd exp.
925     global_ocean.cs32x15.seaice.
926 jmc 1.1585 o pkg/seaice:
927 jmc 1.1586 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
928     of arrays, sign/direction of fluxes; no effect on results.
929     - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
930     in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
931     note: this should have been done before changing celsius2K default.
932     - to keep results unchanged, add back old value of celsius2K in verification
933     exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
934     - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
935     SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
936     value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
937     freezing temp is consistent with value in seaice_growth.F ; this causes
938     differences at machine truncation level: update lab_sea AD output (3/4).
939     o pkg/seaice:
940 jmc 1.1585 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
941     and climsst/sss even when using seaice (to prevent calculation that might
942     use SST on land); does not affect any verification exp.
943     - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
944     of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
945 mlosch 1.1584 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
946     over land (non-legacy code)
947 jmc 1.1585 o vectorize salt_plume package:
948 mlosch 1.1583 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
949     - this code computes plumebk everywhere (also over land), thus requires
950     code to avoid divisions by zero and catch the case of kLev=Nr.
951     - efficiency of salt_plume_frac is still sub-optimal
952 jmc 1.1582 o tools (genmake2):
953     - fix makefile NAME specification (option: -makefile NAME) by adding
954     "-f $MAKEFILE" in few places where it was missing including makedepend
955     command (contribution from Paul).
956    
957 jmc 1.1581 checkpoint63i (2012/01/24)
958 jmc 1.1579 o model/src:
959 jmc 1.1581 - add factorized versions of some EOS code to find_rho.F,
960 mlosch 1.1580 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
961 jmc 1.1581 o model/src:
962 jmc 1.1579 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
963     - change default celsius2K from 273.16 to 273.15
964     - to keep results unchanged, add back old value of celsius2K in verification
965 jmc 1.1581 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
966     global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
967 mlosch 1.1578 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
968     to make TAF generate vectorizable code
969     o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
970     Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
971     have flags that do this more efficiently.
972 mlosch 1.1577 o pkg/diagnostics/diagstats_calc.F
973     - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
974 jmc 1.1576 o pkg/obcs (with exch2):
975     - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
976     and remove code (in obcs_readparms.F) which was based on EXCH of indices
977     (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
978 jmc 1.1574 o pkg/exf and seaice exp:
979     - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
980     so that switching off area & heff advection flags does not affect results.
981     - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
982 jmc 1.1575 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
983     EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
984     results of verification experiments: 1D_ocean_ice_column(fwd),
985     global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
986     and offline_exf_seaice (all 4).
987 jmc 1.1573 o pkg/seaice:
988     - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
989     remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
990     - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
991     but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
992     not multi-dim advection;
993     - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
994     SHORTWAVE_HEATING #undef.
995 mlosch 1.1571 o optim: make Makefile more robust (?)
996 heimbach 1.1572 o pkg/obcs:
997     * fix treatment of obcs_read_pickup for TAF
998 jmc 1.1573 o pkg/shelfice:
999 heimbach 1.1572 * add missing initialisation of num_shifwflx
1000     * new adjoint verification exp. for isomip
1001     * change Prandtl and Schmidt numbers from generic formulations
1002 jmc 1.1573 (in terms of model diffus. and visc.) to separate runtime
1003 heimbach 1.1572 parameters, with Holland and Jenkins (1999) default values.
1004 jmc 1.1570 o pkg/exf (interpolation):
1005     - extended input field (2 rows) near the N & S poles:
1006     * fill in with the symetric value (when even Nb of data in longitude)
1007     * add average value at the poles only for scalar quantities ; for vector
1008     component interpolation, skip the averaging and keep duplicated values,
1009     unless the 2 components have same location (uvInterp=T) in which case
1010     interpolate the 2 components together using S/R EXF_INTERP_UV.
1011     - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
1012     together: this allows to account properly for local orientation when
1013     averaging at N & S pole.
1014     - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
1015     exf-interpolation near N & S poles. Undef by default.
1016     - add debug check/print on 1rst iter if debugLevel >=2.
1017 jmc 1.1569 o pkg/exf:
1018     - change masking flags definition (no longer "parameter"), put them in
1019     common block and set them in S/R EXF_INIT_FIXED.
1020     - change recognized masking flag from s,u,v to c,w,s since the mask
1021     to use (maskC,W,S) depends on position on model grid and has little to
1022     do with scalar/vector difference; fix masking if using P-coordinates.
1023     - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
1024     and update results of exp. global_with_exf (x2).
1025     - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
1026 mlosch 1.1568 o pkg/obcs
1027     - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
1028 jmc 1.1567 o pkg/exf (interpolation):
1029     - assume periodicity in X only if input field cover full longitude range.
1030     - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
1031     and should vectorise).
1032     - fix input lat of the 2 added row (in case we provide N.pole data).
1033    
1034 jmc 1.1565 checkpoint63h (2011/12/30)
1035 jmc 1.1566 o pkg/seaice:
1036     - change declaration of UVM from _RL to _RS in order to get B-grid
1037     uIce,vIce monitor when _RS = real*4
1038 jmc 1.1564 o pkg/offline:
1039     - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
1040     - compute vertical velocity if not read from file (switch on exactConserv
1041     & staggerTimeStep);
1042     - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
1043 jmc 1.1563 o verification:
1044     - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
1045     with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
1046     fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
1047     - update output of exp. global_ocean.cs32x15.viscA4 after changing
1048     grid-file angles (used here for coriolis-3d);
1049     - remove (or gzip) few files not needed to run fizhi-cs experiments.
1050 jmc 1.1567 o pkg/exf (vector interpolation):
1051 jmc 1.1562 - rotate vector component toward local grid-axis orientation using grid-angles
1052     (stored in GRID.h) instead of locally computed rotation angle; keep old code
1053     available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
1054     o pkg/seaice:
1055     - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
1056     undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
1057 jmc 1.1561 o pkg/PKG_OPTIONS.h files:
1058     - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
1059     outside of the #ifdef ALLOW_THISPKG / #endif block.
1060     - update verification/*/code/PKG_OPTIONS.h files.
1061 mlosch 1.1560 o add a verification experiment (offline_exf_seaice/input.seaice) that test
1062     the B-grid LSOR solver
1063 mlosch 1.1559 o pkg/seaice: sort out emissivity and long wave radiation step 2:
1064 jmc 1.1561 - add emissivity for snow and ice as new run-time parameters
1065     (unfortunately) that default to the corresponding exf values; this
1066 mlosch 1.1559 changes results in most verification experiments so that for backward
1067     compatibility these parameter have to be set explicitly to inconsistent
1068 jmc 1.1561 values (ugly);
1069 mlosch 1.1559 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
1070     emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
1071     until we agree how to handle this bug properly
1072 jmc 1.1557 o pkg/exf (interpolation):
1073     - add a set of run-time param ({inputfield}_interpMethod), one for
1074     each interpolated input field, to select the interpolation method
1075     with a value of zero switching off the interpolation;
1076     - print interpolation parameters to standard output;
1077     - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
1078     (to use instead runoff_interpMethod=0 in data.exf).
1079 jmc 1.1558 - simplify default setting of interpolation parameters (for all fields,
1080     set position to match model grid cell-center position, leading to trivial
1081     interpolation in case of regular Lat-Lon grid) and fix for the case of
1082     non-uniform delY.
1083 jmc 1.1557 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1084 mlosch 1.1555 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
1085 jmc 1.1557 this factor is absolutely required, because the lw exitance (= out-going
1086     long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1087 mlosch 1.1555 where the reflectivity rho = 1-emissivity for conservation reasons. Once
1088     this is established, we can remove the CPP-Flag (if we want to).
1089 jmc 1.1557 o pkg/seaice:
1090 mlosch 1.1556 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
1091     ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
1092 mlosch 1.1554 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
1093     what the name implies (and not emissivity*BoltzmannConstant), this means
1094 jmc 1.1557 the old default value of 5.5e-8 now means
1095     5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
1096 mlosch 1.1554 S/R exf_readparms
1097     - FV-discretization of the B-grid LSOR solver, turn on with
1098 mlosch 1.1555 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
1099     of the calling routine dynsolver, so that B and C-grid code look a
1100     little more alike.
1101 mlosch 1.1556 - fix index bugs in ostres.F (B-grid code)
1102 mlosch 1.1553 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
1103 mlosch 1.1552 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
1104     default for SEAICE_emissivity, if useEXF; requires setting a wrong
1105     parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
1106     backward compatiblity
1107     o model/src: use sigmaR in calc_ivdc
1108    
1109 jmc 1.1551 checkpoint63g (2011/12/16)
1110 gforget 1.1550 o pkg/seaice/seaice_growth.F:
1111     fix heat conservation of the coupled ocean-seaice system.
1112     when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
1113     solid vs liquid water treatment is resolved via QNET.
1114     o pkg/seaice/seaice_growth.F:
1115     add missing term for sublimation in saltFlux, which was breaking conservation.
1116     o pkg/seaice/seaice_model.F:
1117     Remove this patholigical case treatment in evolution branch,
1118     where it is un-necessary and breaks conservation.
1119 jmc 1.1557 Update global_ocean.cs32x15/results accordingly for
1120     output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
1121 jmc 1.1549 o model/src:
1122     useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
1123     external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
1124     o pkg/obcs:
1125     modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
1126     tendency for temperature and salinity that is then applied to update
1127     theta and salt in S/R obcs_apply_ts; this requires proper masking of all
1128     horizontal advection and diffusion contributions on the boundary (in
1129     S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
1130     removing the mask in S/R timestep_tracer. The advantage of this approach is
1131     that the updated tracer values include contributions from the surface
1132     forcing and vertical diffusion.
1133 mlosch 1.1548 This modification changes exp4.stevens because of vertical diffusion.
1134 jmc 1.1545 o model/src:
1135 jmc 1.1547 change non-curvilinear grid setting to also work with exch2 + blank tiles:
1136     - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
1137     face dimensions.
1138     - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
1139     as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
1140     and INI_SPHERICAL_POLAR_GRID.
1141     change test-experiment global_ocean.90x40x15:
1142     - split the domain in many more tiles (9x4 tiles of 10x10 each);
1143     - switch to exch2 and remove 1 blank-tile (but only for MPI test).
1144     - update results of both test (std & dwnslp).
1145 jmc 1.1549 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
1146 mlosch 1.1548 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
1147 jmc 1.1547 o model/src:
1148 jmc 1.1546 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
1149     and fix initialisation when using sigma-coords.
1150     o model/src:
1151     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
1152     to their current value at the beginning of forward_step.F": add a new run-time
1153 jmc 1.1545 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
1154     - set doResetHFactors=T in the following test exp:
1155     global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
1156     global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
1157     and tutorial_global_oce_in_p (nonLinFS in p)
1158 mmazloff 1.1543 o pkg/ecco
1159     - added IES cost term
1160 jmc 1.1542 o verification/advect_xz
1161     - scale down the depth by 1/100 (from 200 km to just 2.km)
1162     - add secondary test using divergent flow, r-star and implicit vertical advection.
1163 jmc 1.1544 - add note (check_conserve_TS.txt) and matlab script to check global
1164     conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
1165 jmc 1.1542 o pkg/rbcs:
1166     - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
1167 mlosch 1.1541 o pkg/obcs (Stevens BCs):
1168 jmc 1.1542 - fix various problems in the phase speed computations of the Stevens
1169 mlosch 1.1541 boundary conditions:
1170     - sign error for western and southern boundaries,
1171 jmc 1.1542 - time tendencies were underestimated by factor of dTracerLev and some just
1172 mlosch 1.1541 zero (for multidim advection schemes) -> now estimate time tendencies
1173     from difference between previous (n) time level and the one before (n-1);
1174 jmc 1.1542 this requires storing a field per tracer per boundary, also in the pickup
1175 mlosch 1.1541 files.
1176     - replace deltaTmom in cflMer/Zon computation with dTracerLev
1177     - set default phase velocity to cflMer/Zon
1178     - update verification experiment exp4.stevens
1179 jmc 1.1540 o pkg/generic_advdiff (implicit_r):
1180     - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
1181     (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
1182     - fix implicit vertical diffusion or advection with NonLin FreeSurf
1183     (was using current recip_hFacC instead of future recip_hFacC): set future
1184     recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
1185     solver S/R ;
1186     - fill diagnostics of vertical advective fluxes (computed from tendency)
1187     when using implicit vert. advection;
1188     - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
1189     global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
1190     tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
1191     and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
1192     o pkg/diagnostics:
1193     - add diags for T & S tendency which goes through Adams-Bashforth.
1194    
1195 jmc 1.1539 checkpoint63f (2011/11/30)
1196 mlosch 1.1537 o pkg/obcs/obcs_calc_stevens.F:
1197 mlosch 1.1538 - join some loops to reduce number of if-statements
1198 mlosch 1.1537 - fix a bug in code for northern and southern boundaries.
1199 mlosch 1.1536 o pkg/seaice/seaice_init_varia.F
1200 jmc 1.1539 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
1201 mlosch 1.1536 caused zero ice-velocities for the B-grid code
1202 mlosch 1.1535 o pkg/seaice/seaice_init_fixed.F
1203 jmc 1.1539 - fix a bug in the initialisation of the second metric terms
1204 mlosch 1.1535 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
1205     - this affects all seaice configurations with useCurviLinearGrid = .true.
1206     and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
1207     = .true. (default)
1208     - the only verification experiment affected is global_ocean.cs32x15:
1209     icedyn, seaice, and seaice_dynmix (AD)
1210     o pkg/thsice/thsice_diagnostics_state.F
1211     - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
1212     not contain garbage that can lead to surprises in diagstats_calc.F
1213 jmc 1.1534 o model/src:
1214     - move bi,bj loops inside INTEGR_CONTINUITY ;
1215     - call INTEGR_CONTINUITY directly from forward_step.F
1216     (previously called from momentum_correction_step.F)
1217     - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
1218     forward_step.F and pkg/ecco/the_main_loop.F
1219 jmc 1.1533 o model/src/do_oceanic_phys.F:
1220     - reset addMass to zero only if useICEFRONT ;
1221     - separated k-loop for rhoInSitu calculation ;
1222     - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
1223     and at constant T,S (= WdRHOdP);
1224     NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
1225     of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
1226     transport of locally-referenced potential density);
1227     to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
1228 mlosch 1.1532 o gluemnc:
1229     - replace ncrcat with ncks when adding variables to *.glob.nc
1230     - change the way variables without record dimensions are handled so that
1231     files that have variables with and without record variables can be glued:
1232     add a record dimension with a new unique name to be able to differentiate
1233     between variable with and without a-prior record dimensions. Remove
1234     this record dimension before adding the variable to the *.glob.nc file.
1235     This procedure automatically works also for grid.*.nc files that do not
1236     have any record dimension.
1237 jmc 1.1531 o verification/cpl_aim+ocn:
1238     - generate new reference output on baudelaire (gfortran, mpich2) (previously
1239     from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
1240     o pkg/obcs/obcs_calc_stevens.F:
1241 mlosch 1.1530 - add code for northern and southern boundaries.
1242     - reorder some loops to save some operations and so that drFBar can be scalar
1243 jmc 1.1529 o model/src:
1244     - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
1245     truncation) and add diagnostics for Adams-Bashforth tendency increment.
1246     - update test-exp. AD output:
1247     1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
1248     and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
1249     front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
1250     global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
1251     matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
1252     tutorial_global_oce_in_p, tutorial_global_oce_latlon and
1253     tutorial_plume_on_slope.
1254 mlosch 1.1528 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
1255     that vectorises. This code uses 3 extra 2D fields, F90 array assignments
1256     and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
1257     does not even come with an F77 compiler anymore, this should not be
1258     a limitation
1259    
1260 jmc 1.1527 checkpoint63e (2011/11/06)
1261 heimbach 1.1525 o pkg/seaice adjoint of LSR:
1262     - substantially rework STORE dirs.
1263     - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
1264     this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
1265     and only perform SOLV_MAX_FIXED adjoint iters.
1266 heimbach 1.1526 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
1267     always goes to same record, meaning that the last forward field will be
1268     the one used in the adjoint - an approximation.
1269 heimbach 1.1525 - now produces non-zero LSR-related gradients, and acceptable gradients for
1270     An's zonal (x-z) test case (to be checked in)
1271     - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
1272     (but these are screwed up by the thermodynamics in the first place);
1273     reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
1274     output_adm.txt also reflects changes to seaice_lsr
1275 jmc 1.1527 - global_ocean.cs32x15:
1276 heimbach 1.1525 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
1277     (output_adm.seaice.txt was updated)
1278     * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
1279     (output_adm.seaice_dynmix.txt)
1280 jmc 1.1524 o test-exp. exp4+stevens:
1281     - switch off pTracers and nonHydrostatic (restart problems with NH); update output
1282 jmc 1.1523 o pkg/seaice (lsr solver):
1283     - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
1284     update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
1285     - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
1286     - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
1287     into initial guess for linearised solver; use weight ~ (1/err)^2,4.
1288     - compute (with new S/R) and print initial (+ free-driff sol. if available)
1289     and final residual of linearised system.
1290 mlosch 1.1522 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
1291     (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
1292 mlosch 1.1521 o pkg/obcs: Stevens BCs (still only for east and west)
1293     - fix Stevens BCs by using intermediate velocities of previous
1294     time step as "baroclinic" contribution rather velocity of one grid cell
1295     inside the boundaries; more consistent but makes the entire treatment
1296 jmc 1.1523 more complicated, requires new pickup files and two new S/Rs:
1297 mlosch 1.1521 obcs_copy_uv_n and obcs_save_uv_n
1298 jmc 1.1523 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
1299 mlosch 1.1521 (undefined by default)
1300 jmc 1.1523 - silently move computation of some grid factors into separate loops to
1301 mlosch 1.1521 save some recomputations
1302     - add a hack for non-linear free surface
1303     - add a verification experiment to exp4 that tests this code
1304 mlosch 1.1520 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
1305    
1306 jmc 1.1519 checkpoint63d (2011/10/25)
1307 jmc 1.1516 o pkg/obcs + seaice-dynamics:
1308     - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
1309     solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
1310     values (consistent with an implicit method).
1311     - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
1312     return to older implementation (same results as before); note that none of
1313     the "experimental" OBCS_SEAICE options are implemented in the new version.
1314 jmc 1.1517 - switch test exp. seaice_obcs to use new version (update output).
1315 jmc 1.1516 o pkg/seaice:
1316     - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
1317     - add parenthesis in Water-Ice drag calculations (evp & lsr);
1318     - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
1319 jmc 1.1515 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
1320     - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
1321     and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
1322 dfer 1.1514 o pkg/layers:
1323     - Include potential density as new coordinate (Thanks to David Munday)
1324     o pkg/dic:
1325     - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
1326     carbonate computation/output to CALC_PCO2_APPROX
1327 mlosch 1.1518 o pkg/generic_advdiff
1328 jmc 1.1519 - make TAF generate code that vectorizes:
1329 mlosch 1.1518 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
1330 jmc 1.1519 o model/src:
1331     - improve vectorization also for adjoint code of
1332 mlosch 1.1513 solve_tridiagonal and solve_pentadiagonal. As this requires up to
1333     5 new 3D-fields, this code is only turned on for the combination of
1334 mlosch 1.1518 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
1335     for singular matrix check (only for TARGET_NEC_SX).
1336 mlosch 1.1513 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
1337 jmc 1.1516 ALLOW_AUTODIFF. This flag now needs to be set outside of
1338 mlosch 1.1513 solve_tri/pentadiagonal.F
1339 jmc 1.1512 o pkg/exf:
1340     - fix previous modif in exf_readparms.F (revision 1.66: treatment of
1341     optional namelist EXF_NML_OBCS).
1342     - add many debug-print (to trace down where pkg/cal error msg comes from)
1343 mlosch 1.1511 o pkg/mom_vecinv/mom_vi_hdissip.F
1344     - rearrange loops so that vectorization is improved and in particular
1345 jmc 1.1512 the adjoint routine vectorizes. The code is a little longer now, but I
1346     think easier to read.
1347 mlosch 1.1511 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
1348 jmc 1.1510 o pkg/seaice:
1349     - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
1350 jmc 1.1509 o pkg/exch2:
1351     - alternative code (without tile x tile matrix) for cumulated (global) sum;
1352     used as default; keep using matrix version in adjustment.cs-32x32x1.
1353 jmc 1.1508 o tools/build_options:
1354     - after merging some MPI and/or multi-threads specific optfiles so that
1355     the modified default optfile support both built (using genmake2 -mpi
1356     for the MPI built, using genmake2 -omp for OpenMP built),
1357     move now obsolete optfiles to tools/build_options/unsupported/
1358     (add copy of email sent to support list in doc/optfiles_changes.txt)
1359    
1360 jmc 1.1507 checkpoint63c (2011/09/28)
1361 jmc 1.1506 o pkg/ebm:
1362 jmc 1.1507 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
1363 jmc 1.1506 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
1364 heimbach 1.1504 o pkg/seaice (SItracer pickup)
1365     * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
1366     To be done:
1367     - thorough testing of missing fields in S/R seaice_read_pickup
1368     - thorough matching between generic tracers and specific fields used
1369     (e.g. volume-weighted age, area-weighted age, salinity, ...)
1370 jmc 1.1505 o pkg/grdchk:
1371     - all procs calculate and print finite-difference gradient (for testreport)
1372     - change description output used by testreport;
1373     - AD testing: also compare and report Finite-difference gradient;
1374     => update all output_adm*.txt
1375     o test exp. global_ocean_ebm:
1376     - switch back useRealFreshWaterFlux (no problem anymore with run-off);
1377     and turn on exactConserve; update (fwd) output.
1378 jmc 1.1503 o pkg/seaice (LSR):
1379     - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
1380     - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
1381     * identical results with non-CS topology (but save up to half of EXCH calls)
1382     * no much changes in cs-32 verification tests since no ice at face edges
1383     (differences due to convergence criteria, since nb of iterations changed)
1384     * expect some differences on lat-lon-cap grid.
1385     update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
1386 jmc 1.1502 o pkg/exch2:
1387     - add new CPP option to disable Cumul-Sum matrix (to save storage when using
1388     many tiles); until alternative coding is added, just add a stop.
1389 jmc 1.1501 o pkg/kpp:
1390     - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
1391     to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
1392     o optfiles:
1393     - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
1394     into corresponding standard one, which now support different build:
1395     (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
1396     - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
1397 jmc 1.1500 o pkg/obcs (seaice):
1398     - add missing EXCH for uIce,vIce after applying OBCS;
1399     - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
1400     argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
1401     EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
1402     - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
1403     - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
1404     and eedata.mth for MPI and mutlti-threaded testing.
1405 jmc 1.1499 o pkg/flt:
1406     - make FLT EXCH working with multi-threads (and MPI + multi-threads);
1407     - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
1408     - fix pickup and trajectories + profiles output with multi-threads;
1409     - add parameter to select group of fields to write along trajectory and
1410     profile (default unchanged);
1411     - only call PORT_RAND* function when flt_noise <> 0;
1412     - add multi-threaded test for verification exp. flt_example.
1413     o eesupp/src:
1414     - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1415     - USE_OMP_THREADING: check that number of threads (from eedata) matches
1416     actual number (from env.var. setting).
1417 jmc 1.1498 o pkg/ebm:
1418     - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1419     - add multi-threaded test for verification exp. global_ocean_ebm
1420    
1421 jmc 1.1497 checkpoint63b (2011/08/29)
1422 jmc 1.1496 o pkg/ebm:
1423     - fix sign of runoff;
1424     - update directly forcing fields (Qnet,EmPmR) to use standard
1425     external_forcing_surf.F (remove ebm_forcing_surf.F);
1426     - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
1427     - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
1428     and apply relaxation towards corresponding SST field (2-D map or ZonAver).
1429     - update global_ocean_ebm parameters file data and update output (fwd+ad).
1430 jmc 1.1494 o verification/matrix_example:
1431 jmc 1.1495 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
1432     MPI and mutlti-threaded testing.
1433     o pkg/matrix:
1434     - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
1435     - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
1436     - fix for multi-threaded (remove DATA statement);
1437     - use standard DIFFERENT_MULTIPLE function;
1438     - add MATRIX_OPTIONS.h
1439     o verification/matrix_example:
1440 jmc 1.1494 To allow to split the domain in several tiles, change the domain size
1441     from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1442     Western side) of land points.
1443     o (*_)write_pickup:
1444     - fix few bugs in mypackage_read/write_pickup.F
1445     - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1446     array of length 1 (was caught by compiler syntax-check).
1447 jmc 1.1493 o pkg/diagnostics (velocity potential solver):
1448     - fix initialisation of main diagonal matrix (for overlap values)
1449 jmc 1.1492 o tools/build_options:
1450     - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1451     into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1452     - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1453     * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1454     * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1455     and use "-devel" testreport option for standard testing on baudelaire.
1456 jmc 1.1491 o pkg/grdchk:
1457     - Assume that all gradient-check position are within the same tile
1458     corresponding to global indices (iGloTile,jGloTile) and that
1459     positions (i,j indices or nbeg) are local to this tile;
1460     - set tile local-indices and proc. number according to tile global-indices;
1461     - remove grdchkwhichproc from namelist (retired param);
1462     - send adjoint gradient to all procs so that all procs print it to STDOUT;
1463     - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1464 dimitri 1.1489 o adding package bbl (Bottom Boundary Layer)
1465     description in MITgcm/pkg/bbl/bbl_description.tex
1466     example/test experiment in MITgcm_contrib/bbl
1467 heimbach 1.1488 o adjoint verifications
1468 jmc 1.1490 - changed 5 experiments to multi-tiles
1469 heimbach 1.1488 * global_ocean.90x40x15
1470     * obcs_ctrl
1471     * offline_exf_seaice
1472     * tutorial_dic_adjoffline
1473     * tutorial_tracer_adjsens
1474     changed reference output for those that crossed tile boundaries
1475     (changed choices of gradient check positions)
1476 jmc 1.1490 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1477 heimbach 1.1488 - temporary bug fix in grdchk_loc.F for obcs
1478 jmc 1.1487 o genmake2 & testreport
1479     - add target "obj" (just for OBJFILES files) to Makefile;
1480     - add option to specify FEXTRAFLAGS on command line.
1481 jmc 1.1486 o pkg/mypackage:
1482     - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1483    
1484 jmc 1.1485 checkpoint63a (2011/08/02)
1485 jmc 1.1484 o pkg/diagnostics (velocity potential):
1486     - fix velocity-potential calculation when using OBCS: balance net inflow
1487     at each level (new S/R OBCS_DIAG_BALANCE).
1488     - fix some of the problems with OBCS in stream-function calculation.
1489 mlosch 1.1483 o pkg/exf/exf_readparms.F
1490 jmc 1.1484 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1491 mlosch 1.1483 EXF_NML_OBCS) more consistent, so that you need not have these lists
1492     in data.exf when they are not used.
1493 mlosch 1.1481 o optim/optim_readdata.F:
1494     - add some output about obcs variables that might help debugging
1495 mlosch 1.1482 - add a check about nvarlength
1496 mlosch 1.1480 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1497 jmc 1.1479 o pkg/diagnostics (velocity potential):
1498     - fix mask for OBCS (still problems in stream-function with OBCS);
1499     - add specific parameter (default = main code CG2D params) for solver;
1500     - in case of poor convergence, use solution corresponding to lowest residual.
1501 mlosch 1.1478 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1502     adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1503     and should be avoided where possible.
1504 jmc 1.1477 o model/src (rStar):
1505     - include r* effect on reference-state (PhiRef) in totPhiHyd
1506     (so that it's really the potential anomaly at the cell center);
1507     affect solution only if z* with full pressure in EOS.
1508     - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1509     update output (because of z* in totPhiHyd and viscA4 changes);
1510     - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1511     @ constant r) until interpolation at constant r is implemented.
1512     o pkg/diagnostics
1513     - fix RCENTER diagnostics in case cell center is not at interface middle
1514 mlosch 1.1476 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1515     this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1516     that THETA and SALT are "conservative temperature" and "absolute
1517     salinity"
1518     o pkg/ctrl
1519     - fix computation of endrec in s/r ctrl_init_rec
1520     - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1521 mlosch 1.1475 o pkg/seaice/seaice_growth.F
1522     - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1523     remove then obsolete STORE directives
1524     - fix STORE directives for tice and tices, so that only the
1525     appropriate part of the fields are stored (and not the entire
1526 jmc 1.1477 field); update global_ocean.cs32x15.seaice AD output.
1527 mlosch 1.1475 - cosmetic changes: adjust CPP flags and indentation for better
1528     legibilty
1529     o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1530     Chris Wilson)
1531 jmc 1.1474 o pkg/gmredi:
1532     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1533     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1534    
1535 jmc 1.1485 checkpoint63 (2011/07/11)
1536 jmc 1.1472 o pkg/exch2:
1537     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1538     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1539     (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1540     increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1541 jmc 1.1470 o pkg/diagnostics:
1542     - deal with pairs of post-processed diags which are computed together; in
1543     particular, re-order list of diags within 1 file to save 2nd computation.
1544     - add S/R to compute velocity stream-function (called after velocity-potential
1545     calculation) from divergence free transport -> new diagnostics "PsiVEL".
1546 jmc 1.1471 - add parameter to select grid-point location where PsiVEL == 0.
1547 jmc 1.1470 o eesupp/src:
1548     new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1549     (specific S/R needed with exch2 topology - for now, just print an error msg)
1550 heimbach 1.1468 o pkg/shelfice
1551     - Implement friction velocity-dependent transfer coefficients following
1552     Holland and Jenkins, JPO, 1999
1553     Original code by M. Losch with small modifs.
1554     Enable with CPP option SHI_ALLOW_GAMMAFRICT
1555     and runtime flag SHELFICEuseGammaFrict
1556 jmc 1.1467 o verification lab_sea & global_ocean.cs32x15:
1557     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
1558     does not miss some dependencies (but is slower) and also works with many files
1559     (default makedepend limitation for AD built).
1560     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
1561 jmc 1.1466 o pkg/diagnostics:
1562     - add run-time parameter "useMissingValue" (def=False) to fill land-point
1563     (i.e., where mask=0) with MissingValue ; used only in MNC output file.
1564     This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
1565     - Extend the use of "missing_value" setting from data.diagnostics for the case
1566     of counter-diagnostics (where fraction-weight is zero). This applies both to
1567     MNC and MDS output files.
1568 gforget 1.1465 o pkg/seaice/seaice_growth.F:
1569 ifenty 1.1469 - add 'a priori' cap of latent heat flux based on actual mass considerations
1570     when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1571     non-legacy seaice_solve4temp.
1572     - add diagnostic of the residual sublimation freshwater flux (the freshwater
1573 jmc 1.1470 flux taken from the ocean if the total actual latent heat fluxes exceed
1574 ifenty 1.1469 the maximum)
1575 gforget 1.1465 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1576     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
1577     - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
1578     SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
1579     - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
1580     - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
1581 ifenty 1.1464 o verification 1D_ocean_ice_column:
1582     made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
1583     update results
1584 jmc 1.1461 o pkg/diagnostics:
1585     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
1586     which are not filled-up but computed from other diags ; In this case, the mate
1587     diag points to the primary (filled-up) diag to used for post processing.
1588     - Update Velocity-potential computation using post-processed diag framework.
1589 jmc 1.1463 ==> Change the ordering of fields and time-periods in MDS output file
1590 jmc 1.1462 when using periodic averaging: now writes one time record with the full set
1591     of fields for this time period, then the next time reccord (it used to be
1592     one field with the full set of time records then the next field).
1593 jmc 1.1463 Note: this is now similar to NetCDF (MNC) output file. <==
1594 jmc 1.1461
1595 jmc 1.1460 checkpoint62z (2011/06/21)
1596 heimbach 1.1456 o adjoint monitor:
1597     - Add adjoint monitor output for packages exf, seaice
1598 heimbach 1.1457 and update relevant testreport output
1599 gforget 1.1455 o pkg/seaice:
1600     - re-order diags inits so that they appear in order in available_diagnostics.log
1601     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
1602     area/heff/hsnow preceeding thermodynamic growth/melt.
1603     - modified diag: SIdA; output actual effect, as the description states.
1604     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
1605     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
1606 jmc 1.1459 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
1607 gforget 1.1455 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
1608     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
1609 jmc 1.1459 - added diagnostics for seaice generic tracers (SItr*).
1610 gforget 1.1455 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
1611     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
1612 heimbach 1.1458 I. Fenty: 18-Jun-2011:
1613     Minor changes to seaice package:
1614     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
1615     added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
1616 jmc 1.1459 - Differentiated "regularization variables" from "floor variables"
1617 heimbach 1.1458 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
1618     * hiceMin became SEAICE_hice_reg (old hiceMin)
1619     (with _reg meaning regularization variable)
1620     - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
1621     so as to ensure energy conservation when going between phases
1622 jmc 1.1459 - A22 was not used anywhere
1623 heimbach 1.1458 2) Changed regularization procedure for heffActual and hsnowActual to ensure
1624     well-boundedness and smooth adjoint in seaice_growth.F
1625     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
1626     because the old regularization always set heffActual >= 0.05 cm
1627     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
1628 jmc 1.1459 on AREA when HEFF > 0.
1629     - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
1630     requiring that DISABLE_AREA_FLOOR *not* be defined
1631 heimbach 1.1458 Affected verifications:
1632     - 1D_ocean_ice_column (output.txt output_adm.txt)
1633     - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
1634 jmc 1.1453 o pkg/diagnostics:
1635     - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
1636     - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
1637     (was _RL, now integer) with option = 0 to retrieve all levels.
1638 jmc 1.1454 - add pieces of code to compute velocity potential at each level (new diagnostics
1639     PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
1640     for now, using same params as CG2D (target-resisual, max Nb of iter ...).
1641 jmc 1.1459 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
1642     diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
1643     and in diagnostics_fract_fill.F (do not need a valid pointer for the
1644     diagnostics counter-mate); check that definition of counter-diagnostic
1645     includes a valid counter-mate (in diagnostics_set_levels.F).
1646 jmc 1.1452 o model/src (rStar):
1647     - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
1648     affect solution only if z* with full pressure in EOS;
1649     update output of test-exp global_ocean.90x40x15.
1650     o pkg/seaice:
1651 gforget 1.1451 - introduce siEps=1e-5 parameter
1652     - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
1653     - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
1654 jmc 1.1452 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
1655 gforget 1.1451 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
1656     as well as ice cover age and ridging index (attached to AREA).
1657 jmc 1.1452 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
1658     SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
1659 gforget 1.1451 Up to SItrMaxNum=3 tracers can be used simultaneously.
1660     o pkg/salt_plume:
1661 jmc 1.1452 -introduce SPsalFRAC run time parameter that sets the fraction of the
1662     salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
1663     that gets vertically redistributed (fluxed down) by pkg/salt_plume.
1664 jmc 1.1450 o model debug options:
1665     - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
1666     in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
1667     - Refine debug-msg printing selection (3 new levels):
1668     debugMode : controls printing of debug messages (sequence of S/R calls).
1669     debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
1670     debLevZero = 0 ; /* level of disabled aux. msg printing */
1671     debLevA = 1 ; /* level of minimum aux. msg printing */
1672     debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
1673     debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
1674     debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
1675     debLevE = 5 ; /* level of extensive debug printing */
1676     New debugLevel default: with default debugMode value (=F),
1677     = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
1678     and if debugMode=T, default debugLevel = 4 (debLevD).
1679     Relation with previous settings:
1680     debLevB (=2) corresponds to former debLevA (=1)
1681     debLevD (=4) corresponds to former debLevB (=2)
1682     Note:
1683     a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
1684     b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
1685     to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
1686     - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
1687     detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
1688 jmc 1.1449 o pkg/obcs:
1689     - change OBCSfixTopo default from True to False (should not change the results);
1690     keep OBCSfixTopo=T in verification-exp. seaice_obcs.
1691 jmc 1.1448 o pkg/thsice:
1692     - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
1693     2nd layer seaice sublimation (unlikely to happen)
1694     - use Interior mask for OBCS in thsice_advection.F (similar to what is
1695     done in gad_advection & seaice_advection).
1696 heimbach 1.1447 o adjoint:
1697     bug fix spotted by Gael Forget:
1698     seaice_advection and thsice_advection still had
1699     legacy CPP options to avoid CS corner updates for adjoint
1700 jmc 1.1446 o pkg/seaice:
1701     => Change some of the defaults (2011/05/29):
1702     - change SEAICEuseFluxForm default (from False to True)
1703     - change DIFF1 default (from 0.004 m/s to 0. m/s)
1704     And print warnings if DIFF1 is not set in data.seaice and centered
1705     avection scheme is used without any diffusion.
1706     also:
1707     - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
1708     - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
1709     - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
1710     other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
1711     #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
1712     update results of test exp.:
1713     lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
1714     output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
1715     output_adm.noseaicedyn (SEAICEuseFluxForm=T)
1716     offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
1717     seaice_obcs: output (SEAICEuseFluxForm=T)
1718     and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
1719     for standard fwd & AD lab_sea tests (to keep the same output).
1720 gforget 1.1445 o pkg/seaice/seaice_growth.F:
1721 jmc 1.1446 - use Ian Fenty's capping formulas for actual ice
1722 gforget 1.1445 thickness thoughout EVOLUTION branch.
1723     - put treatment pathological case #2) in CPP brackets
1724     (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
1725 jmc 1.1446 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
1726 gforget 1.1445 o pkg/seaice:
1727     - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
1728 jmc 1.1446 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
1729     also pass fac as a param, which can be 1. (to update the tendency
1730 gforget 1.1445 field) or the time step (to update the field itself).
1731 jmc 1.1446 - seaice_advdiff.F: for multidim, call seaice_diffusion with
1732 gforget 1.1445 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
1733     seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
1734 jmc 1.1446 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
1735 gforget 1.1445 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
1736 jmc 1.1444 o pkg/seaice:
1737     diffusion with centered advection scheme (diffus.F & advect.F):
1738     - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
1739     to just compute the laplacian of input-field.
1740     - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
1741     - fix flux-form version in diffus.F to conserve tracer.
1742     update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
1743     machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
1744    
1745 jmc 1.1443 checkpoint62y (2011/05/26)
1746 gforget 1.1442 o pkg/seaice:
1747 jmc 1.1443 - seaice_growth.F : in EVOLUTION branch, always include
1748 gforget 1.1442 a_QSWbyATM_cover in qnet (as it should be).
1749     - verification/global_ocean.cs32x15 : update results accordingly
1750 jmc 1.1443 (output.seaice.txt output_adm.seaice.txt).
1751 jmc 1.1441 o pkg/seaice + obcs:
1752     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
1753     equivalent of assuming no tracer gradient outside the OB region.
1754     update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
1755     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
1756     after changes above);
1757     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
1758     only at OB location (instead of over a band of OLx width).
1759     o pkg/seaice:
1760     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
1761     (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
1762 jmc 1.1438 o pkg/obcs:
1763 jmc 1.1439 - split header file "OBCS.h" into 4 separated files:
1764     OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
1765     Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
1766 jmc 1.1440 (contain no conditional statement which depends on OBCS options).
1767     - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
1768     to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
1769 jmc 1.1439 o ctrl, cost, grdchk & autodiff pkgs:
1770     - make options file more standard (like other {PKG}_OPTIONS.h file but
1771     with AD_CONFIG.h); clean-up some of the included header files.
1772     o pkg/obcs:
1773 jmc 1.1438 - do not mask tracer when applying OB (tracer == 0 could generate problems)
1774     - apply tracer OB values to tracer field only at OB location (instead of
1775     over a band of OLx width)
1776     - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
1777     - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
1778     obcs_apply_tloc.F & obcs_apply_sloc.F
1779     o obcs in model/src:
1780     - call OBCS_APPLY_W only if NonHydrostatic.
1781     - call OBCS_APPLY_ETA only if NonLinFreeSurf.
1782     - reset dEtaHdt and wVel to zero outside OB interior region ;
1783     - leave tracer unchanged outside OB interior region: This has no effect
1784     on the solution but just to prevent unrealistic tracer value outside OB.
1785     - zero out velocity outside OB interior region: This has no effect on
1786     the solution but just to prevent unrealistic velocity outside OB.
1787 jmc 1.1437 o obcs and non-lin free-surf:
1788     move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
1789     and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
1790     + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
1791     this fixes missing EXCH + get consistent eta OB value (+ fix restart).
1792     update results of test-exp. exp4(nlfs).
1793 jmc 1.1436 o exp4 (nlfs) test-exp:
1794     use OBC for Eta at Western & Eastern OB (to test prescribing Eta
1795     with NonLin-FreeSurf); update output.nlfs.txt
1796 jmc 1.1435 o obcs and 2d/3d solver norm:
1797 jmc 1.1436 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
1798     and outside OB interior region (will allow to place OB further inside the
1799     domain). Depending on the domain, can affects cg2d-Norm (previous
1800 jmc 1.1438 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
1801 jmc 1.1435 and cg3d-Norm (previous Norm was computed before canceling OB terms),
1802     e.g. in tutorial_plume_on_slope.
1803     - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
1804 jmc 1.1433 o pkg rbcs:
1805     - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
1806     - add capability to apply relaxation to horizontal velocity uVel & vVel.
1807 mlosch 1.1432 o pkg/grdchk: add gradient check for control variable xx_shifwflx
1808     o pkg/shelfice/shelfice_init_fixed.F
1809     fix CPP-flag combinations
1810 heimbach 1.1434 o pkg/seaice: Merge iceage code of Pierre Rampal
1811     * update/change/correct ice age calculations
1812 jmc 1.1436 * add age updates for pathological cases
1813 heimbach 1.1434 Probably needs more testing...
1814 mlosch 1.1432
1815 jmc 1.1431 checkpoint62x (2011/05/13)
1816     o pkg/mom_vecinv:
1817 jmc 1.1433 high-order vorticity scheme: use interior masks (maskInW & S)
1818 jmc 1.1431 to zero-out (outside OB) gradient of vorticity.
1819 jmc 1.1430 o verification exp.:
1820     turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
1821     hs94.128x64x5 and seaice_obcs ; update results.
1822 jahn 1.1429 o pkg/obcs:
1823     fix bug in OBeta for YZ sections in obcs_exf_load.F
1824 jmc 1.1430 o pkg/ctrl, pkg/shelfice, and optim:
1825     - add new control variable xx_shifwflx (fresh water flux underneath ice
1826     shelves). This is almost as tedious as obcs-ctrl, because the
1827 mlosch 1.1427 variables needs its own mask.
1828 jmc 1.1430 - add a cost function term that penalizes the deviation of xx_shifwflx
1829 mlosch 1.1427 from the first guess (zero) in analogy to other control variables
1830 heimbach 1.1426 o pkg/shelfice:
1831     - start basic adjoint
1832 jmc 1.1430 o pkg/ctrl:
1833 mlosch 1.1425 - remove extra 2D field "for good measure" when initializing in
1834     ctrl_set_globfld_[xy/xz/yz].F
1835 mlosch 1.1424 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1836     - improve error messages in ctrl_set_unpack_*
1837 jmc 1.1423 o OBC implementation in momentum:
1838     use interior masks (maskInC,W & S) in momentum S/R:
1839     - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1840     - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1841     - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1842     - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1843     Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1844     (and also with Leith/Smagorinsky harmonic-viscosity).
1845     Update output of experiment dome and exp4 (+nlfs).
1846 jmc 1.1421 o exp4 test-exp:
1847 jmc 1.1422 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1848     and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1849     at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1850     time-varying OB at Western-side for wVel (NonHyd); update output.
1851 jmc 1.1421 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1852 jmc 1.1422 and biharmonic-viscosity ; also use prescribed time varying OB.
1853 jmc 1.1421 o pkg/obcs:
1854     fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1855 jmc 1.1420 o model/src:
1856     - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
1857     - initialise startTime & nIter0 with unlikely values: allows to set one
1858     from the other without ambiguity.
1859 jmc 1.1419 o seaice_obcs test-exp.:
1860     add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
1861 jmc 1.1418 o pkg/obcs:
1862     - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
1863     no longer needed with maskInC,W,S in pkg/generic_advdiff.
1864 ifenty 1.1417 o pkg/seaice:
1865 jmc 1.1418 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
1866 ifenty 1.1417 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
1867 jmc 1.1418 - fixed bug in the initialization of sea ice salinity variable HSALT
1868 ifenty 1.1417 in seaice_init_varia.F (removed dependence on ICE2WATR)
1869 jmc 1.1416 o fizhi-cs test exp.:
1870     switch reference output convention for these 2 non-standard test-exp,
1871 jmc 1.1418 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
1872 jmc 1.1416 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
1873     reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
1874 jmc 1.1415 o model/inc:
1875     - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
1876     of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
1877 ifenty 1.1414 o pkg/seaice:
1878     - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
1879     o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
1880 ifenty 1.1417 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
1881     and initial HSALT
1882 ifenty 1.1414
1883 jmc 1.1413 checkpoint62w (2011/04/26)
1884 jmc 1.1412 o pkg/mom_fluxform:
1885     - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
1886     - use parameter "sideDragFactor" in no-slip BC side-drag part.
1887     - update output of exp. global_ocean.90x40x15
1888 jmc 1.1411 o pkg/mom_vecinv:
1889     mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
1890 jmc 1.1413 o update seaice exp.:
1891     use more consistent parameter values (remove "backward compatability only":
1892     ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
1893     related to thermodynamics seaice. Update output (fwd+AD) of exp.:
1894     1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
1895 jmc 1.1411 o update test-exp global_ocean.90x40x15:
1896     o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
1897     o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
1898     o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
1899     o turn on zStar & viscA4 in standard set-up (dir input/)
1900     and update output files: output.txt & output.dwnslp.txt
1901 jmc 1.1409 o new AD-test experiment: obcs_ctrl
1902     (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
1903     o pkg/dic:
1904     fix two bugs in handling water vapour pressure in carbonate chemistry
1905     and air-sea fluxes. Found by Val Bennington and Galen McKinley
1906     (add DIC Option = WATERVAP_BUG to recover old results)
1907     update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
1908 dimitri 1.1408 o adding allowInteriorFreezing option to check for water below freezing point
1909     at depth and bring the negative heat anomaly to the surface level
1910 jmc 1.1409 o pkgs _fields_load:
1911     - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
1912     - use new S/R GET_PERIODIC_INTERVAL in pkgs:
1913 jmc 1.1410 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
1914     rbcs to get interpolation weights and time reccord number.
1915 jmc 1.1409 - fix multi-threading in aim_fields_load.F
1916     - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
1917 jmc 1.1407 o external_fields_load:
1918     new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
1919     interpolation weights) to use in a periodic time-series ; do not divide by
1920     time-step to convert to integer:
1921     - this fixes case where externForcingPeriod is not multiple of time-step
1922     (Thanks to Christopher L. Wolfe)
1923     - this fixes case where externForcingPeriod is an odd multiple of time-step
1924     (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
1925     store index of time-record which is currently loaded:
1926     - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
1927     - needed for the adjoint but not yet used because of extensive recomputations;
1928     (to be fixed soon)
1929    
1930 jmc 1.1405 checkpoint62v (2011/04/02)
1931 ifenty 1.1406 o verification/1D_ocean_ice_column added to test Ian Fenty's
1932     pkg/seaice_growth.F modifications for improving sea ice code differentiability
1933 jmc 1.1405 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
1934     (new velocity statistics after changing maskInW & maskInS definition)
1935 jmc 1.1404 o pkg/generic_advdiff with OBCS:
1936     use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
1937     equivalent to assumption of no tracer gradient outside the OB region.
1938     This will affect the results if using obcs+biharmonic diffusion.
1939     update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1940 jmc 1.1403 o pkg/obcs:
1941     change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
1942     (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
1943     in Interior region. No impact on solution but affects Velocity monitor stats.
1944 heimbach 1.1402 o pkg/ptracers (adjoint)
1945 jmc 1.1403 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
1946 heimbach 1.1402 tape file for each tracer
1947 jmc 1.1403 o model/inc/src and pkg/autodiff: add parameters that allow to turn
1948     of parts of the adjoint code at run time. For now, there are only
1949     useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
1950     parameters are set in data.pkg.
1951     This is the lazy coward's version of doing this, but still useful for
1952     debugging. In order to do it right, everything needs to be moved to
1953 mlosch 1.1401 pkg/autodiff.
1954 jmc 1.1403 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
1955 mlosch 1.1401 the end; this fixes the adjoint balancing code for open boundaries.
1956 mlosch 1.1399 o pkg/ctrl:
1957     - change behavior of xx_${varname}period to be analogous to exf-conventions:
1958     xx_${varname}period = 0., means time-independent control part
1959 jmc 1.1403 xx_${varname}period = -12., means one-year-periodic monthly control part
1960 mlosch 1.1399 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1961     clean up ctrl_init a little, remove unused variables
1962 mlosch 1.1400 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1963 mlosch 1.1399 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1964    
1965 mlosch 1.1398 checkpoint62u (2011/03/15)
1966 jmc 1.1397 o model/src:
1967     - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1968     h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
1969     - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
1970     INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
1971     o pkg/ctrl/obcs/ecco:
1972 mlosch 1.1396 - remove obsolete, unused, and partially broken code:
1973 jmc 1.1397 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1974 mlosch 1.1396 ALLOW_CTRL_OBCS_BALANCE
1975 jmc 1.1397 - put a stop statement into ecco/cost_obcsvol.F, but also add
1976 mlosch 1.1396 cost_obcsvol to ecco_ad_diff.list
1977 mlosch 1.1395 o pkg/ecco: fix counting cost function contributions for obcs (code
1978     by Matt M.) and diffkr for diagnostics
1979 heimbach 1.1394 o pkg/ecco, pkg/ctrl, pkg/grdchk:
1980     add cost penalty terms for initial uvel, vvel, eta controls
1981     and I/O for prior error files
1982 jmc 1.1393 o pkg/mdsio:
1983     move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1984     (new argument) to check for tiled file in mdsioLocalDir : this fix the
1985     restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
1986 mlosch 1.1392 o pkg/ctrl:
1987     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
1988     ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
1989     unused and superfluous variables
1990     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
1991 mlosch 1.1391 o pkg/ecco
1992     - enable adjoint of Stevens OB
1993 jmc 1.1393 o pkg/ctrl/ecco/grdchk:
1994 mlosch 1.1390 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
1995 mlosch 1.1391 Fortunately, we do not have any tests for the numerous cpp-flagged
1996 mlosch 1.1390 option of "obcs as control parameters" so we will never know
1997     if this is an improvement (but at least now things compile).
1998     - remove an obsolete initialization from ecco_cost_init_barfiles.F
1999 jmc 1.1393 - fix some problems within never used ifdefs to make the code compile
2000 jmc 1.1388 o pkg/obcs:
2001     - Refine Interior mask definition to work with more complex OB (e.g.
2002     if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
2003     read in Interior mask from file. Check if Interior mask is consistent
2004     with OB list of indices.
2005 heimbach 1.1387 o pkg/seaice
2006     - beginning code for a seaice tracer package,
2007     but currently only used for seaice age: SEAICE_AGE
2008     SEAICE_num = 4
2009     iTracer = 1: area-weighted ice age
2010     = 2: volume-weighted ice age
2011     = 3, 4: template for one-year vs. multi-year ice
2012     data.seaice has new namelist SEAICE_PARM03 for arrays related to
2013     SEAICE_num
2014    
2015 heimbach 1.1386 checkpoint62t (2011/03/05)
2016 jmc 1.1383 o pkg/obcs:
2017 jmc 1.1384 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
2018     then normal component. This ensures that the normal component is set
2019     correctly even when it conficts with tangential setting from an other OB.
2020     Affects results of test-experiment seaice_obcs: update the output.txt
2021     o pkg/obcs:
2022 jmc 1.1383 - add code to monitor statistics of dynamical fields at OB.
2023     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
2024     - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
2025     - change default: balance the Net inflow through all OB (instead of balancing
2026     each OB separately); keep the old method if setting OBC_balanceFacX < 0.
2027     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
2028     to match Nortern OB inflow (OBCS_balanceFacN=0).
2029 dimitri 1.1382 o pkg/seaice:
2030     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
2031 dimitri 1.1381 o pkg/seaice (seaice_growth v 1.113):
2032     - reverting seaice_growth to v 1.111 in order to have code with exact bit
2033     compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
2034     CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
2035     runtime flag SEAICEareaFormula is kept but is inactive
2036 jmc 1.1380 o model/src:
2037     - add new param to scale curvilinear grid distance and area when using
2038     a different sphere radius from the grid-files.
2039     - test/check multi-threads EXCH applied to local variable (cg2d_x)
2040 heimbach 1.1385 o adjoint:
2041     - enable adjoint of Stevens OB
2042     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
2043     (a bit delicate because of potentially modified adj. common block structure;
2044     current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
2045 jmc 1.1380
2046 jmc 1.1379 checkpoint62s (2011/02/15)
2047 dimitri 1.1381 o pkg/seaice (seaice_growth v 1.112):
2048 gforget 1.1378 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
2049 jmc 1.1379 computing the ice cover tendency from effective thickness tendencies. Include
2050     Ian Fenty's formula.
2051     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
2052     SEAICEareaFormula.
2053 gforget 1.1378 - simplify notations for the various d_HEFF/d_AREA terms.
2054 jmc 1.1377 o pkg/gmredi:
2055     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
2056     from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
2057     add a verification test-run (front_relax.bvp) to test GM_useBVP.
2058 dimitri 1.1381 o pkg/seaice (seaice_growth v 1.111):
2059 gforget 1.1376 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
2060 jmc 1.1379 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
2061     also melt ice.
2062 jmc 1.1377 o pkg/seaice:
2063 gforget 1.1375 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
2064     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
2065 jmc 1.1374 o pkg/cheapaml:
2066     - from Nico Wienders: New version of this package.
2067 jmc 1.1372 o pkg/flt:
2068     - add CPP options to prevent floats to re-enter the opposite side of
2069     a periodic domain (default: keep periodicity)
2070 jmc 1.1370 o pkg/gmredi:
2071     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
2072     (needed for multi-dim advection).
2073 jmc 1.1371 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
2074 jmc 1.1370 o model/src:
2075     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
2076 heimbach 1.1373 o tutorial_tracer_adjsens
2077     - extend to NLFS and replace maskC by hFacC
2078     (change reference output accordingly)
2079 jmc 1.1370
2080 jmc 1.1369 checkpoint62r (2011/01/24)
2081 jmc 1.1368 o testreport:
2082     - add option -deloutp (-do) to remove output file after successful run
2083     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
2084     extract exact list of procs from this file ; adjust COMMAND by
2085     replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
2086 mlosch 1.1367 o pkg/ecco: replace old ineffective way of penalizing deviations from
2087     first guess (of obcs) with code by Matt Mazloff
2088 jmc 1.1368 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
2089 mlosch 1.1366 exf/cal
2090     - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
2091     and handle case of obcs?period == 0
2092     Not affected by these changes: There is still an inconsistency in
2093 jmc 1.1368 the computation of start/endrec for the obcs variables for ALLOW_CAL
2094 mlosch 1.1366 defined (see comment by Menemenlis, 7-Mar-2003)
2095     - make S/R ctrl_get_gen_rec return something meaningful even if
2096     ALLOW_CAL is not defined
2097 jmc 1.1368 - ctrl_getobcs?: simplify code so that it does not need to use
2098 mlosch 1.1366 S/R exf_swapfields
2099 jmc 1.1365 o testreport:
2100     allow to test MPI with different number of processors for each experiment:
2101     create file "SIZE.h.mpi" in each build dir.
2102     Note: update of "-command" argument not yet implemented.
2103 gforget 1.1364 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
2104     alleviate the need for additional 3D tapes when using
2105     the non-inear free surface in the adjoint. This is done
2106 jmc 1.1368 by adding an 'update' of hfacc etc. to their current
2107     value at the beginning of forward_step.F.
2108 mlosch 1.1362 o pkg/seaice
2109     seaice_lsr: move stress-divergence computations out of outer pseudo-
2110 jmc 1.1363 timestepping loop
2111 mlosch 1.1362 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
2112     up, so that the calls of the ctrl_* subroutines are really at the end
2113     of the routine.
2114 jmc 1.1363 o pkg/gmredi:
2115     allow to specify a 2-D horizontal map and a 1-D vertical profil
2116     as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
2117 gforget 1.1364 o pkg/seaice:
2118     move lsr iterations from seaice_dynsolver to seaice_lsr.
2119     o pkg/seaice:
2120     reduce memory footprint of seaice mutldim advection tapes,
2121     by using a 2D tape independent of the generic_advdiff ones,
2122     and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
2123 mlosch 1.1362
2124 jmc 1.1361 checkpoint62q (2010/12/29)
2125 jmc 1.1360 o model/src:
2126     - check horizontal grid-spacing for unset or zero/negative values.
2127     - change AD test hs94.1x64x5 to be truly a 2-D set-up.
2128 jmc 1.1359 o pkg/flt:
2129     - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
2130     - precision of input and output files set according to readBinaryPrec
2131     and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
2132     - initial float position from tiled file was not converted to index space
2133     (looks like a bug): fixed to make it similar to initial pos. global file.
2134 jmc 1.1358 o global_ocean.cs32x15:
2135     change SIZE.h of AD set-up to get same tiling as with MPI.
2136     Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
2137     o model/src:
2138     add flag to control printing of domain fields (bathymetry, hFac ...) in
2139     ini_mask_etc (call to plot_fieds_xy*).
2140     o pkg/thsice:
2141     if useEXF, some forcing fields are not valid in overlap: fixed by computing
2142     over the interior only + apply EXCH at the end (like with SEAICE advection).
2143 jmc 1.1357 o pkg/mdsio:
2144     - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
2145     to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
2146     - change barrier call for safe multi-threads access to 3-D shared buffer.
2147     - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
2148     - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
2149     remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
2150 jahn 1.1356 o pkg/flt:
2151     - add fourth-order Runge-Kutta integration
2152     - add basic exch2 support (only 1 facet supported so far!)
2153 jmc 1.1355 o pkg/mdsio+rw:
2154     new S/R to read local (or tile independent) vector (read counterpart of
2155     mds_writevec_loc, and front-end write_glvec_rl/rs).
2156 gforget 1.1354 o global_ocean.cs32x15: additional input_ad.seaice experiment
2157     that uses pkg/seaice rather than pkg/thsice.
2158     (using multidim advection for seaice)
2159 jmc 1.1353 o towards more F95 syntax for array specification in namelist:
2160     - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
2161     of all verification experiments.
2162     e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
2163     was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
2164     - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
2165 gforget 1.1352 o global_ocean.cs32x15: additional input.seaice experiment
2166     that uses pkg/seaice rather than pkg/thsice.
2167 jmc 1.1353
2168 jmc 1.1350 checkpoint62p (2010/12/17)
2169 gforget 1.1351 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
2170     to THSICE_SIZE.h to avoid conflict with pkg/seaice.
2171     o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
2172     allow for use of multim. advection in seaice adjoint.
2173 mlosch 1.1349 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
2174     - first attempt to close budgets by taking into account the freshwater
2175 jmc 1.1350 flux implied by the sublimation of snow and ice. So far only the
2176 mlosch 1.1349 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
2177     SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
2178 jmc 1.1348 o eesupp/src:
2179     new S/R with new option (NML_EXTENDED_F77) to change array specification
2180     from F95 standard to commonly accepted extended F77 form.
2181     This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
2182     and to revert back to the original syntax (with -DNML_EXTENDED_F77)
2183     for less tolerant f77 compiler (e.g., pgf77, g77).
2184 jmc 1.1346 o globalFiles:
2185     commented out in parameter file "data" since it's not safe with MPI
2186     (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
2187     in this case); no longer commented out in restart test (tst_2+2).
2188     o add adTapeDir to specify a special directory where adjoint tapes are
2189     written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
2190 mlosch 1.1345 and cannot be used together with mdsioLocalDir.
2191 jmc 1.1343 o nesting pkgs:
2192     - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
2193     - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2194     - add parameter files + utils dir + output from short run on beagle.
2195 gforget 1.1344 o pkg/seaice:
2196     fix seaice_growth.F store directives; update results of exp. lab_sea.ad
2197 jmc 1.1343 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
2198 mlosch 1.1342 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
2199    
2200 jmc 1.1341 checkpoint62o (2010/11/25)
2201 jmc 1.1340 o pkg/exf:
2202     - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
2203 jmc 1.1341 o pkg/seaice:
2204     - seaice_ocean_stress: split a loop for better vectorization of the
2205     adjoint code
2206 mlosch 1.1337 - seaice_growth.F: fix bug in conservation of freshwater connected to
2207 mlosch 1.1338 capping of heff, put contribution into d_HEFFbyNEG
2208 mlosch 1.1337 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
2209     by something more sensible (parameters that are what their name implies)
2210     - change some defaults, so that by default exf-parameters are used for
2211     things like rhoAir, cpAir,latent/sensible heat parameters, in order
2212     to reproduce the old results, many data.seaice now contain funny values
2213     for cpAir and latent heat of sublimation
2214 jmc 1.1341 o packages_readparms.F: move exf_readparms up in line so that
2215 mlosch 1.1337 exf-parameters are visible for other packages (e.g. seaice)
2216 jmc 1.1336 o debugMode & debugLevel=2:
2217     - differentiate between debugMode & debugLevel=2:
2218     debugMode: controls printing of debug messages (sequence of S/R calls).
2219     debugLevel: controls printing of algorithm intermediate results and stats.
2220     - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
2221     => allows to print debug-stats without all sequence of call messages.
2222     - switch control of debug print from debugLevel to debugMode in many S/R.
2223     o pkg/obcs (obcs-sponge):
2224     fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
2225     call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
2226 jmc 1.1335 o pkg/generic_advdiff:
2227     - record overlap minimum size for each advection scheme;
2228     - refine criteria on overlap minimum size;
2229     - check and stop (in gad_check) if overlap size is too small.
2230     o pkg/obcs:
2231     - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
2232     once, in ptracers_implicit.F)
2233     - with seaice: remove test on empty file name in obcs_apply_seaice (always
2234     apply OB values when tile has OB)
2235 jmc 1.1334 o model/src, coriolis setting:
2236     - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
2237     useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
2238     files (selectCoriMap=3) with any grid.
2239     - add parameter "fPrime" for constant second Coriolis coeff (default=0).
2240     o pkg/seaice/seaice_growth.F:
2241     a few cosmetic changes that reduce the number of lines of code
2242 mlosch 1.1332 o pkg/obcs: add boundary conditions following Stevens (1990)
2243     - the code follows old MOM/NAOSIM code
2244     - so far it is only implemented for the eastern and western boundaries
2245     and NOT for pTracers
2246 jahn 1.1331 o pkg/rbcs:
2247     - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
2248     beginning of the first rbcs forcing period.
2249     - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
2250     offline package, i.e., one file per time, labeled by iteration number;
2251     deltaTrbcs sets the timestep with which the data was generated;
2252     rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
2253     - rbcsForcingCycle=0 makes forcing non-cyclic.
2254     - make arithmetic safe for negative times and odd forcing periods.
2255    
2256 jmc 1.1330 checkpoint62n (2010/11/09)
2257 mlosch 1.1327 o pkg/seaice:
2258 jmc 1.1329 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
2259     o pkg/obcs:
2260     New S/R to copy tracer value from the OB location to narrow band region
2261     (width = same as overlap) beyond the OB: preserve OB value (needed for
2262     high-order scheme) which were overwritten by EXCH call if in overlap
2263     region. Applied to theta, salt, ptracer and advected seaice variables.
2264     With seaice: use maskInC in similar way as in gad_advection.F,
2265     in seaice_advection.F and advect.F.
2266     Update output of experiment seaice_obcs and change exp4 to test OBCS with
2267     4th order Adv.Scheme. for pasive salt and ptracer.
2268     o tools/genmake2:
2269     - when looking for an optfile (not specified), only search for Fortran compiler
2270     (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
2271     - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
2272     (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
2273     - set default for CPP to "cpp -traditional -P" (was the case without specifying
2274     an optfile, but otherwise default was just "cpp".
2275     - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
2276     - when "CC" is not set in the optfile, look for possible C compiler
2277     (instead of just setting CC=cc)
2278     - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
2279     => add a ".F" to ".o" rule for source files with no "#include" (such as
2280     port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
2281     - move gfortran before g77 in list of possible Fortran compiler (consistent
2282     with reference compiler switch from g77 to gfortran)
2283     o pkg/seaice:
2284     o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
2285 mlosch 1.1327 seaice_check that stops the model, when the CPP flag is used.
2286     o seaice_growth.F: make capping of ice volume conserving by returning the
2287     capped ice as freshwater to EmPmR. This does not change the verification
2288     experiments but will change runs where the capping is acutally active
2289 jmc 1.1326 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
2290     (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
2291     global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
2292     lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
2293     o tools/genmake2:
2294     - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
2295     - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
2296     - clean previous genmake log files before anything else.
2297     - change Makefile to remove testreport log files (*.tr_log) and genmake log
2298     files only with "CLEAN" target (instead of "Clean");
2299 jmc 1.1324 o pkg/generic_advdiff:
2300     Change OBCS in multiDim advection (gad_advection.F):
2301     Use maskInC to prevent intermediate update of tracer-field in OB regions,
2302     thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
2303     which were applying future time-step OB values.
2304     This way, all explicit calculations use current-time-step OB values
2305     (simpler and more consistent).
2306     Affects results when set-up uses time-varying OBC and multi-dim advection;
2307     update output of experiment seaice_obcs.
2308 jmc 1.1323 o pkg/seaice:
2309     move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
2310     this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
2311     SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
2312     Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
2313     but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
2314     unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
2315 dfer 1.1322 o pkg aim (2010/10/26):
2316     - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
2317     formulation with obliquity, eccentricity, ... as run-time parameters,
2318     - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
2319     upward shortwave radition at the surface (all-sky and clear-sky).
2320 jmc 1.1319 o pkg/obcs:
2321 dimitri 1.1321 - writing sections with globalFiles=T does not work: switch to tiled-files
2322     when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
2323     - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
2324     - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
2325 jmc 1.1319
2326 jmc 1.1318 checkpoint62m (2010/10/21)
2327 mlosch 1.1316 o pkg/seaice: vectorize seaice_solve4temp.F
2328     - move iterations loops outside of i/j-loops
2329     - requires 2D arrays for TB and effConduct
2330 jmc 1.1318 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
2331 mlosch 1.1316 modified in this routine
2332     - a little bit of clean up, adjusting indentation, etc.
2333 jmc 1.1318 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
2334     performance and '**TWO' by '**2' (because TWO is a float),
2335 mlosch 1.1316 replaced ONE, ZERO
2336 jmc 1.1314 o eesupp/src:
2337     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
2338 gforget 1.1313 o pkg/seaice/seaice_growth.F
2339 jmc 1.1314 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
2340     merging process. The merged routine has two branches, and one activates the 'evolution'
2341 gforget 1.1313 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
2342     In summary, here is what the '10/10 revision' did consist of
2343 jmc 1.1314 part 1: seaice_growth.F revisions 1.71 to 1.75
2344 gforget 1.1313 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
2345 jmc 1.1314 The emphasis here was on improving readability (e.g. by trying to use meaningful
2346 gforget 1.1313 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
2347 jmc 1.1314 part 1.5:
2348     - revising the lab_sea experiment to make it a more useful (i.e. stable
2349     and representative of an actual model run). This was done by generating a
2350     (winter) pickup to start from, switching back the main experiment dynamic
2351 gforget 1.1313 solver from evp to lsr, having one of the experiments use the free drift solution.
2352 jmc 1.1314 part 2: seaice_growth.F revisions 1.76 to 1.85
2353 gforget 1.1313 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
2354 jmc 1.1314 - Sorting out the various fields units and sign (set early on and reset at the end)
2355     to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
2356     fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
2357     - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
2358 gforget 1.1313 and simplifying logical expressions to further improve readibility.
2359     part 3: seaice_growth.F revisions 1.86 to 1.89
2360     - Re-organize the blocks of code more logically.
2361     - Merging the '_if.F' pieces that add something new.
2362 jmc 1.1314 o pkg/thsice:
2363     - vectorize thsice_solve4temp and thsice_get_exf.
2364 mlosch 1.1312 Problem: thsice_solve4temp has an unvectorizable statement that
2365     might also be problematic for TAF
2366 jmc 1.1314 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
2367     does not change the verifcation experiment, but will change all
2368 mlosch 1.1312 experiments that have this flag undefined (not tested in verification);
2369     a little reorganization to save a few 2D fields and recomputations
2370 heimbach 1.1315 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
2371 heimbach 1.1317 - 2nd step: fix some store dirs
2372     o seems to work somewhat, i.e. using ifort but not g77
2373     o likely cause are incomplete init. or recomputation
2374     o start verification/global_ocean.cs32x15/input_ad.thsice
2375 jahn 1.1311 o pkg/obcs: add support for exch2
2376     - the position of the boundary and prescribed values are specified using
2377     a global domain with exch2 facets stacked
2378     - in x for N,S boundaries (like W2_mapIO=-1)
2379     - in y for E,W boundaries (so E,W boundaries do not overlap)
2380     o pkg/mdsio: add support for writing global sections with exch2
2381     file layout is as for obcs described above:
2382     - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
2383     - for y-z sections, facets are stacked in y
2384 jmc 1.1309 o pkg/thsice:
2385 mlosch 1.1310 - change a few routines for better vectorization: thsice_albedo.F,
2386     thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
2387     not affected, but in particular the latter routine has changed
2388     dramatically (not necessarily easier to read now).
2389     - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
2390 jmc 1.1309 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
2391 gforget 1.1308 o verification/lab_sea:
2392     - overhaul of the forward model experiments. The main motivation
2393 jmc 1.1314 for this revision is that lab_sea has proven quite fragile (when
2394 gforget 1.1308 changing the sea-ice code, and switching platforms) to a point
2395     when failures were very hard to attribute to specific code problems.
2396 jmc 1.1314 - the suspected reason for this fragility is noise amplification by evp so,
2397 gforget 1.1308 to start with, we decided to replace evp with lsr in the main experiment.
2398     - the input.lsr experiment thus became obsolete and was removed.
2399 jmc 1.1314 - it was replaced with the input.fd experiment that uses an
2400 gforget 1.1308 analytical "free drift" solution as the ice velocity field.
2401     - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
2402     will hopefully allow us to discriminate problems due to dynamic solvers
2403     from problems due to the thermodynamic code. input.salt_plume (lsr) allows
2404     us to test additional options, along with the salt plume package.
2405 jmc 1.1314 - Finally a pickup was generated (at the end of a one year run) to
2406 gforget 1.1308 make the tests more representative of an actual model run. Previously
2407     the tests starting point was a 1m thickness of ice everywhere.
2408 jmc 1.1314 o pkg/seaice:
2409 gforget 1.1308 - introducing S\R seaice_freedrift.F that compute the
2410 jmc 1.1314 analytical solution to an approximate ice momentum
2411 gforget 1.1308 equation (i.e. the simple stress/coriolis balance).
2412     - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
2413 jmc 1.1314 of the free drift velocity field, and enable its use.
2414     To actually use the free drift solution as the model ice
2415     velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
2416 mlosch 1.1307 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
2417    
2418 jmc 1.1306 checkpoint62l (2010/10/04)
2419 jmc 1.1305 o pkg/seaice:
2420     -fix the USE_ORIGINAL_SBI version (for variable freezing point);
2421     -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
2422     version (with USE_ORIGINAL_SBI undef);
2423 mlosch 1.1304 o add hooks for new packages OASIS, the package will follow
2424     (hooks exclude the seaice pkg for now)
2425 gforget 1.1303 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
2426 jmc 1.1305 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
2427 gforget 1.1303 rather than mdsio_readvector.F/mdsio_writevector.F, within
2428     adread_adwrite.F to read/write adjoint-related tapes to disk.
2429 jmc 1.1305 o eesupp and pkg/mdsio: ALLOW_WHIO
2430     Option to write/read 2D fields to files including tiles halos.
2431     The main purpose is for adjoint related "tape I/O".
2432 gforget 1.1302 The secondary purpose is for debugging phases.
2433     A word on those rather specifically intended purposes.
2434     The code was meant to be stripped down to the bare minimum.
2435 jmc 1.1305 Typically, there is a unique and basic mapping to the global
2436 gforget 1.1302 buffer (tile by tile, then proc by proc, then level by level), and
2437     byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
2438 jmc 1.1305 meant to generate user friendly outputs of various shapes and forms.
2439 gforget 1.1302 Rather it is intended, for the knowledgeabale developers,
2440     to be largely independent of the many mdsio options, to allow
2441 jmc 1.1305 outputs of tiles+halos in debugging phases and in adjoint runs,
2442 gforget 1.1302 and to allow some flexibility in tuning (adoint) I/O depending on each
2443 jmc 1.1305 file system behavior. With regard to tuning, most of the potential knobs
2444 gforget 1.1302 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
2445     to specify directories, to specify the typical size of I/O calls, etc.)
2446     are not yet included, and will be added if they prove useful.
2447 jmc 1.1300 o pkg/seaice:
2448 jmc 1.1301 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
2449     o pkg/seaice:
2450 jmc 1.1300 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
2451     code (seaice_budget_ice_if.F) which enable to recover old standard
2452     code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
2453     temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
2454     o model/src (rStar):
2455     use simple average (not area weighted) of rStarFac at U,V point when using
2456     vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
2457     update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
2458 jmc 1.1299
2459 jmc 1.1298 checkpoint62k (2010/09/17)
2460 heimbach 1.1297 o adjoint
2461     * changed verification/global_ocean.cs32x15 ; adjoint now tests
2462     Adams-Bashforth 3 + NLFS + RSTAR
2463     * some more modifs required for ECCO-GODAE v4
2464 dimitri 1.1296 o pkg/seaice
2465     add SEAICE_AGE_VOL option to use volume instead of area for
2466     integrating SEAICE_AGE
2467 jmc 1.1295 o model/src:
2468     first check-in of sigma & hybrid-sigma coordinate code ; also includes
2469     non-linear free-surface parts ; but pressure-gradient not yet coded.
2470 jmc 1.1294 o pkg/ptracers:
2471     option for ptracer to convert Salt Relax into additional EmP.
2472     tested in exp. global_ocean.90x40x15.dwnslp (update output)
2473    
2474 jmc 1.1293 checkpoint62j (2010/08/25)
2475 jmc 1.1292 o pkg/ggl90:
2476     other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
2477 mlosch 1.1291 o pkg/dic: car_flux.F, phos_flux.F
2478     - reduce number of exp-calls in order to improve performance
2479 jmc 1.1292 - clean up a little (replace fields by their macros, etc., fix
2480 mlosch 1.1291 typo in CPP-flag)
2481 gforget 1.1290 o pkg/ggl90: minor changes
2482     - GGL90diffKrS was removed --> always use GGL90diffKr
2483     - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
2484 jmc 1.1292 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
2485     (commented out for now)
2486 gforget 1.1290 - change in max/min operations to ensure that smoothing is ok
2487     - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
2488     - always use diffKrNrT as background profile (i.e. never use diffKr field)
2489 mlosch 1.1289 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
2490 mlosch 1.1286 o pkg/dic:
2491 mlosch 1.1288 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
2492     vectorization
2493 mlosch 1.1287 - small bug fix in insol for the unlikely case of a cartesian grid
2494     - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
2495     + now vectorize, which also removes adjoint recomputations;
2496     + replace integer maksp1 by _RL maskp1
2497 mlosch 1.1288 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
2498 mlosch 1.1286
2499 jmc 1.1285 checkpoint62i (2010/07/21)
2500 jmc 1.1284 o pkg/flt:
2501     - with OBCS: stop floats which enter the OB region
2502     o model/src:
2503     - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
2504     for implicit vertical advection.
2505 jmc 1.1283 o pkg/seaice:
2506     - account for melting in seaice age evolution.
2507 jmc 1.1284 - remove double counting of seaice ridging effect on seaice age.
2508 jmc 1.1283
2509 jmc 1.1282 checkpoint62h (2010/06/18)
2510 jmc 1.1281 o pkg/exch2:
2511     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
2512     o tools/genmake2
2513     - remove "-pdefault" option: redundant with the use of "packages.conf";
2514     - remove file pkg/pkg_default : set the default as a pkg group
2515     ("default_pkg_list") defined in pkg/pkg_groups;
2516     - fix for case pkg/pkg_depend is missing (was hanging before);
2517     - add option "-pgroups" to specify a different pkg_groups than the default.
2518 jmc 1.1280 o verification/adjustment.cs-32x32x1:
2519     add a "minimal" set-up test (code_min & input_min) which only compiles
2520     eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
2521 jmc 1.1279 o tools/genmake2
2522     - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
2523     - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
2524 mlosch 1.1277 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
2525     files are nearly the same anyway.
2526     Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
2527     - redefinition of tau(i,i) (by a factor of ustar)
2528     - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
2529     - replace rhonil by rhoConstFresh in computation of evap (bug fix)
2530     - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
2531 jmc 1.1278 - replace
2532 mlosch 1.1277 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
2533     shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
2534     by
2535     shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
2536     (changes results)
2537 jmc 1.1278 -> exf_bulkformulae v1.22,
2538 mlosch 1.1277 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
2539     (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
2540 jmc 1.1278 output.txt 1.63
2541 mlosch 1.1277 offline_exf_seaice: output.seaicetd.txt 1.7
2542     seaice_obcs: output.txt 1.10)
2543     Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
2544     -> exf_bulkformulae v1.23,
2545     unfortunately requires updating lab_sea.salt_plume (6 matching digits),
2546     and global_ocean.cs32x15.icedyn (only 11 matching digits)
2547 jmc 1.1278 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
2548 jmc 1.1276 o adjoint of exch-1:
2549     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
2550     (note: was already like this when using EXCH-2) and remove flow dir
2551     and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
2552     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
2553     - update pkg/exch2 diff list.
2554    
2555 jmc 1.1275 checkpoint62g (2010/05/19)
2556 jmc 1.1274 o eesupp/src (exch-1):
2557     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
2558     and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
2559     (renamed to exch1_*rx_cube.F).
2560     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
2561     to call new exch1 S/R ; update Makefile and .cvsignore.
2562     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
2563     exch2_xy_rx later)
2564     Note: after updating your code, need to run "make clean" in eesupp/src
2565 jmc 1.1273 o test experiment bottom_ctrl_5x5:
2566 jmc 1.1274 new output_adm.txt with fewer grdchk & less monitor output.
2567 jmc 1.1273 o model/src:
2568     remove the call to ini_cori in initialise_varia.F (just keep the usual one
2569 jmc 1.1274 in initialise_fixed.F). More consistent with coriolis & horizontal grid
2570 jmc 1.1273 beeing treated in the same way (ini_grid is not called a 2nd time).
2571 jmc 1.1274 o pkg/exf:
2572 mlosch 1.1272 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
2573 mlosch 1.1271 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
2574 mlosch 1.1272 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
2575     - cosmetic changes to exf_bulkformulae.F to make it look more like
2576     exf_bulk_largeyeager04.F
2577 jmc 1.1270 o eesupp/src (exch-1):
2578     - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
2579     - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
2580     array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
2581     (even without using MPI).
2582     - Message mode: move RecvAck setting (indicator of buffer being ready)
2583     from send_put to recv_get S/R (was useless before, but not sure if
2584     it's much more useful now);
2585 jmc 1.1273 - Switch the order of sync: MPI-proc 1rst and then threads;
2586 jmc 1.1270 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
2587 jmc 1.1273 - fix AD code for communication mode ='get' (but not used).
2588 jmc 1.1269 o model/src:
2589     initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
2590     not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
2591 mlosch 1.1268 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
2592 mlosch 1.1267 o pkg/ctrl: require a specific set of control variables and exf-flags for
2593     adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
2594 gforget 1.1264 o model/src:
2595 jmc 1.1266 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
2596     1rst forward sweep, to avoid over-writing output files during recomputations
2597     recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
2598     b) 2nd version:
2599     - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
2600     - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
2601     writePickupAtEnd) + seaice & ptracers output;
2602     - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
2603 jmc 1.1265 o model/src:
2604 gforget 1.1264 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
2605 jmc 1.1263 o pkg/exch2:
2606 jmc 1.1265 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
2607 jmc 1.1263 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
2608 jmc 1.1262 o pkg/autodiff & exch2:
2609     process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
2610     (for now, only if ALLOW_EXCH2 is defined).
2611 jmc 1.1261 o pkg/autodiff:
2612 jmc 1.1265 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
2613 jmc 1.1261 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
2614     + clean-up comments (_RS is not always real*4)
2615     - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
2616     - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
2617     was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
2618 jmc 1.1260 o testreport (AD-tests):
2619     no longer link files from dir "../input" (1rst link files from
2620     "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
2621    
2622 jmc 1.1259 checkpoint62f (2010/04/29)
2623 mlosch 1.1258 o model/src/the_main_loop.F:
2624     adjust store directives for seaice evp and multicategory according to
2625     pkg/ecco/the_main_loop.F
2626 heimbach 1.1256 o adjoint:
2627 jmc 1.1260 global_sum_ad was incomplete (noted many times by many people ;)
2628 heimbach 1.1256 nice description by Jean U. as follows:
2629 jmc 1.1260 * allreduce(var) in global_sum.F can be interpreted as
2630     reduce(sum) followed by broadcast of sum.
2631     * The adjoint of that is
2632     sum(adjoint) followed by broadcast(summed adjoint value)
2633 heimbach 1.1256 or in other words, allreduce(sum, adjoint vars)
2634     We were missing the sum(adjoint)!
2635     Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
2636     (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
2637     The fix should produce 16-digit accuracy between
2638     single-CPU multi-tile (e.g. nSx=2, nPx=1) and
2639     multi-CPU single-tile (e.g. nSx=1, nPx-2)
2640     We'll probably change this yet again shortly
2641 jmc 1.1257 o eesupp/src:
2642     - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
2643 dimitri 1.1255 o pkg/icefront
2644     - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
2645     specification of addmass array based on a 2D field, which is added
2646     at bottommost wet level at each horizontal location.
2647 jmc 1.1254 o model/src:
2648     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
2649     layout; (not always compatible with delX,delY setting; commented out for now).
2650 jmc 1.1253 o pkg/exch2:
2651     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
2652     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
2653    
2654 jmc 1.1252 checkpoint62e (2010/04/15)
2655 jmc 1.1251 o pkg/obcs:
2656     - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
2657 jmc 1.1250 o pkg/dic:
2658     -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
2659     (note: not presently tested in any forward verification exp.)
2660     update tutorial_global_oce_biogeo AD output file.
2661     o pkg/exf:
2662 gforget 1.1249 - account for the variation of albedo as a function of zenith angle
2663 jmc 1.1250 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
2664 jmc 1.1248 o build_options:
2665     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
2666     o pkg/dic:
2667     change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
2668     - use binary pickup file for restart;
2669     - initialise atmos-CO2 box from dic_pCO2 parameter;
2670     - fix multi-threaded.
2671 jmc 1.1247 o pkg/rbcs:
2672     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
2673     change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
2674     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
2675     and update output.txt
2676 jmc 1.1246 o pkg/kpp:
2677     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
2678     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
2679 jmc 1.1248 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
2680 jmc 1.1246 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
2681     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
2682     KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
2683 dfer 1.1244 o pkg/offline:
2684 jmc 1.1245 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
2685     (bug was added in version 1.10 on 2007-08-23).
2686     o pkg/offline:
2687 dfer 1.1244 - no need to specify periodicExternalForcing, etc ... to use offline pack
2688     - offline input files no longer just single prec --> parameter offlineLoadPrec
2689 heimbach 1.1242 o verification/lab_sea:
2690 jmc 1.1245 change AD test to multi-tile setup and update all 4 AD output.
2691 heimbach 1.1242 NOTE: while cost function values remain very similar,
2692     gradients are very different, although gradient checks are self-consistent
2693     Should try to get to the bottom of this (cost function summation order?)
2694 jmc 1.1241 o pkg/dic:
2695     in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
2696     a weakness of TAF that drops part of double precision in log10 derivative.
2697 jmc 1.1243 <= changes removed since problem has been fixed in current TAF version 1.9.71
2698 jmc 1.1241 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
2699 jmc 1.1240 o pkg/ecco:
2700     add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
2701     update all 4 lab_sea AD output.
2702    
2703 jmc 1.1239 checkpoint62d (2010/03/22)
2704     o build_options:
2705     remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
2706 jmc 1.1238 o remove unbalanced quote (single or double) in commented line of source code
2707     (may cause some warning with some preprocessor/makedepend versions).
2708     o pkg/seaice:
2709 jmc 1.1237 fix seaice_model.F for adjoint (gael) and update AD results of experiments
2710     lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
2711 jmc 1.1236 o testreport:
2712     add option '-runonly' (short: '-ro') to just do the run part (without make).
2713 jmc 1.1235 o eesupp: remove JAM communication code (obsolete).
2714 jmc 1.1234 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
2715     (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
2716     to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
2717     (update also the output).
2718    
2719 jmc 1.1233 checkpoint62c (2010/03/02)
2720 jmc 1.1232 o tools/build_options :
2721     move (some) old optfiles from build_options/ to build_options/unsupported/
2722 gforget 1.1231 o model/src and pkg/exf
2723     surface relaxation -- separating data and data.exf options
2724     The point is to ensure that we specify the surface relaxation
2725     either in data or in data.exf (but not half and half) and to
2726     avoid an accidental relaxation to 0 (which happened if a time
2727     scale was specified but the file name was left empty)
2728 gforget 1.1230 o model/src model/inc and pkg/mom_common
2729     ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
2730     => addition to the viscosity field as computed by others schemes
2731 jmc 1.1229 o tools/build_options:
2732     - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
2733     but keep the former optfile for few weeks for smooth transition
2734 gforget 1.1228 o pkg/ecco
2735     - allow user defined cost function contributions
2736 dfer 1.1322 CPP: ALLOW_USERCOST_CONTRIBUTION
2737     USAGE: compute contributions in cost_usercost_all.F
2738 gforget 1.1228 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
2739     the two options are complementary.
2740 gforget 1.1227 o pkg/smooth
2741     - migration from contrib to the main repository
2742 jmc 1.1229
2743 jmc 1.1226 checkpoint62b (2010/01/26)
2744 jmc 1.1225 o pkg/monitor:
2745     - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
2746     (in case someone forgot to update customized pieces of code)
2747     o nonHydrostatic:
2748 jmc 1.1224 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
2749     - add a simple 2-D experiment (short_surf_wave) to test it.
2750     o pkg/icefront:
2751     adding the shell of, and the hooks to, a new package that
2752 dimitri 1.1223 will model melting and freezing of vertical glacier ice fronts
2753 jmc 1.1224 o momentum:
2754 jmc 1.1222 add diagnostics of momentum tendency from Hydrostatic pressure gradient
2755     (without surf.pressure term: would need a 2nd filling since implicit term).
2756 jmc 1.1224 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
2757     two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
2758     cannot deal with the former
2759 jmc 1.1220 o cleaning:
2760 jmc 1.1222 - remove all (except OpenAD) old TLM output from results_ad dirs.
2761 jmc 1.1220 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
2762     - comment out maskH definition (replaced by maskInC)
2763     o pkg/monitor:
2764     - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
2765 jmc 1.1225 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
2766 jmc 1.1220
2767 jmc 1.1219 checkpoint62a (2010/01/15)
2768 jmc 1.1218 o model/src:
2769     - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
2770 jmc 1.1217 o pkg/diagnostics:
2771     - add optional level number diagnostics (i.e., level number to be define
2772     explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
2773     - strictly check for valid parser-code(10) ;
2774     - check if adding diag to the list from the right place.
2775 jahn 1.1216 o pkg/longstep:
2776     - change parameters and fix tracer conservation with rstar/nonlinear free surface
2777 jmc 1.1215 o diagnostics:
2778     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
2779     S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
2780 jmc 1.1214 o pkg/diagnostics:
2781     - Add option for writing vertical integral (sum of selected levels) of an output
2782     field instead of writing output field levels. Activate this option on a per
2783     output-file basis, by setting the 2nd character of fileflag to 'I'.
2784     - Add field-specific information relative to level integral in 3rd postion
2785     of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
2786     vertically (x level-thickness x hFac), "r"=same but without hFac.
2787 jmc 1.1213 o do_the_model_io:
2788     - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
2789     in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
2790     writing pickups and stopping.
2791     o pkg/diagnostics (for now, only with mdsio):
2792     - write time information to meta file (and modify accordingly rdmds.m) :
2793     time-averaged diagnostics output: write starting and ending time of the
2794     time-averaging interval ; snap-shot diagnostics output remains unchanged;
2795 jmc 1.1212 o pkg/timeave:
2796     - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
2797     always Nr), now assumed to be equal to number of levels of averaged field;
2798     only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
2799     o pkg/sbo:
2800     - fix ocean bottom pressure global-average & 2-D time-ave output (was
2801     neither initialised nor filled).
2802     - add starting iteration in suffix of global-average output file
2803     (to avoid over-writing the file after a restart)
2804     - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
2805     o time-average:
2806     - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
2807     (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
2808     ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
2809     this fix DIC_COST cumulative-time array (previously: bi,bj,k)
2810     - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
2811     - fix missing accumulation for pkg/opps.
2812     - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
2813     (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
2814     - fix initialisation of time-ave vars and do only full time-step increment
2815     (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
2816 jmc 1.1211 o pkg/layers:
2817     - use standard RW pkg S/R to write the output
2818     and remove local write_fld version (which had a problem).
2819     - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
2820     - fix LAYERS_CALC argument list.
2821     o pkg/timeave:
2822     - store cumulative-time in a simple tiled array (drop the level index)
2823     - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
2824 jmc 1.1210 o pkg/ocn,aim_compon_interf
2825     - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
2826    
2827 jmc 1.1209 checkpoint62 (2009/12/23)
2828 jmc 1.1208 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
2829     (was not previously tested in any other exp.)
2830 jmc 1.1207 o pkg/monitor:
2831     - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
2832 jmc 1.1209 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
2833 jmc 1.1207 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
2834     - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
2835     - change del2 calculation.
2836     - use interior masks (instead of maskH, <- to be remove).
2837     - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
2838     o mask & obcs:
2839     - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
2840 jmc 1.1209 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
2841 jmc 1.1207 (called after packages_init_fixed)
2842 jahn 1.1206 o pkg/obcs:
2843     - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
2844     Fixes bug in obcs+exf with nSx*nSy.GT.1
2845     - fix multi-tile handling in obcs balance code
2846 jmc 1.1205 o nonHydrostatic:
2847     - Implement AB-3 for non-hydrostatic vertical momentum ;
2848     (change ordering of var. stored in pickup file when using NH)
2849     - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
2850     - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
2851     (in prep. for new NH free surface form).
2852 jmc 1.1204 o pkg/obcs:
2853     add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
2854 jmc 1.1209 o model/src:
2855 jmc 1.1204 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
2856    
2857 jmc 1.1203 checkpoint61z (2009/12/01)
2858 jmc 1.1202 o nonHydrostatic:
2859     Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
2860     a spurious source of energy in simple baroclinic adjusment test case.
2861     Update all non-hydrostatic exp output.
2862     o model/src (3-d solver):
2863     Change again 3-D solver free-surface RHS term when exactConserv=T:
2864     simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
2865     (which was not the case with previous formulation).
2866     To recover previous version, just reset "oldFreeSurfTerm" to previous value.
2867     Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
2868     o nonHydrostatic:
2869     - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
2870     for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
2871     - change 3-D solver to work with r* (for now, only with linear free-surf.)
2872     - add few debug diagnostics (cg3d_x, residual)
2873 jmc 1.1201 o model/src:
2874     fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
2875     update output of exp. global_ocean.cs32x15.viscA4
2876 jmc 1.1200 o update output of exp. global_ocean.cs32x15.icedyn after removing
2877     #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
2878     o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2879 mlosch 1.1199 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
2880     for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
2881 mlosch 1.1198 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
2882 jmc 1.1200 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
2883     runtime flag useSRCGSolver. Modify verification experiment global_with_exf
2884     to test this code
2885 jmc 1.1197 o pkg/cd_code:
2886     Change defaut D-grid time-stepping to get the same for D-grid momentum as for
2887     C-grid momentum. D-grid velocity used to be stepped forward in time with
2888     Adams-Bashforth only on surface pressure term. Tests show that using AB on
2889     D-grid coriolis term improves stability (as expected from CD-scheme paper).
2890     To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
2891     Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
2892     lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
2893     tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
2894     Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
2895 jmc 1.1204 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
2896 jmc 1.1196 o pkg/obcs:
2897 jmc 1.1197 - fix bug in initialisation (broken since Oct 1rst modification)
2898 jmc 1.1196 for useOBCSprescribe without useEXF.
2899    
2900 jmc 1.1203 checkpoint61y (2009/11/15)
2901 mlosch 1.1194 o pkg/seaice
2902     - change (once again) the discretization for the evp solver: rather than
2903     squaring the averages of strain rates, average the squares to give
2904     a better approximation to VP behavior (in simple test); this breaks
2905     verification experiments that use EVP (lab_sea and lab_sea.hb87)
2906     --> update outputs
2907 jmc 1.1195 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
2908 mlosch 1.1193 to improve vectorization of adjoint code on TARGET_NEC_SX
2909 dfer 1.1192 o verification/vermix:
2910 mlosch 1.1194 - change vermix to a more "classical" 1d column with high vertical
2911     resolution, seasonal heat flux forcing and constant wind forcing
2912     --> update outputs
2913 mlosch 1.1190 o pkg/seaice
2914     - fix diagnostics of principal stress components for EVP
2915     - add optional diagnostics of non-linear convergence for LSOR solver
2916 mlosch 1.1191 - make maximum zeta a runtime parameter
2917 jmc 1.1189 o model/src (3-d solver):
2918     Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
2919     which consisted in removing the Surf. Non-Hydrostatic pressure from the
2920     whole column and adding it to Eta (inspired from Casualli, 1999):
2921     Only affects 3-D solver initial guess and only if using ExactConserv,
2922     but tests did show a degradation of solver convergence. For this reason,
2923     decide to disable this piece of code.
2924     to recover previous version, just set zeroPsNH = exactConserv (line 78).
2925     Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
2926 jmc 1.1188 o pkg/ggl90:
2927     - fix previous modif (unfortunatly has not been documented here).
2928 mlosch 1.1182 o pkg/seaice/autodiff:
2929 mlosch 1.1185 - add CPP flag to include clipping of zeta in EVP code;
2930     although clipping of zeta is not necessary for EVP and not recommended
2931     it was done by default, now clipping is disabled by default
2932 mlosch 1.1184 - modify computation and store zetaC/Z in seaice_evp for TAF
2933 mlosch 1.1183 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
2934 mlosch 1.1190 - change seaice_calc_viscosities/strainrates for better
2935 mlosch 1.1183 vectorization after AD by TAF
2936 jmc 1.1187 - rearrange common blocks in SEAICE.h once again for easier dumps of
2937 mlosch 1.1182 adjoint output, adjust adcommon.h and g_common.h
2938     - change flux form of default advection scheme for better vectorization
2939     of adjoint code
2940     - modify lab_sea/input.lsr to test the flux form of default advection
2941     scheme
2942 mlosch 1.1181 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
2943     transition in checkpoint61r)
2944    
2945 jmc 1.1203 checkpoint61x (2009/10/19)
2946 heimbach 1.1179 o adjoint: adding two new verification experiments
2947     * tutorial_global_biogeo: an online dic sensitivity experiment
2948     (work with G. Forget)
2949     * tutorial_dic_adjoffline: an offline dic sensitivity experiment
2950     (an update of the Dutkiewicz et al., 2006 paper)
2951     Both use the same CO2FLUX cost function, but different controls
2952     Gradient checks look good, but some recomp. could still be traightened out
2953     Should add xx_dic control variable to test at some point
2954 jmc 1.1178 o model/src:
2955     add run-time parameters to check and/or mask initial Temp & Salt
2956 jmc 1.1177 o pkg/ptracers:
2957     apply zonal filter (if used) to all passive tracers
2958    
2959 jmc 1.1203 checkpoint61w (2009/10/12)
2960 heimbach 1.1175 o adjoint:
2961     * update and finish work on adjoint of dic package (G. Forget)
2962     * start adjoint of offline package
2963     * bug fix for cube-sphere TLM code (active_file_g.F)
2964 jmc 1.1173 o tutorial_global_oce_optim:
2965     now tested with 4 tiles (change data.grdchk and update output_adm.txt)
2966 jmc 1.1174 and add SIZE.h_mpi for MPI testing
2967 mlosch 1.1172 o pkg autodiff
2968     - fix bug in autodiff_restore
2969     - make genmake2 remove comments and empty lines from ad_input_code.f in
2970     order to reduce file size (new script file remove_comments_sed)
2971 jmc 1.1171 o allows to specify vertical profile of vertical viscosity (viscArNr)
2972 mlosch 1.1170 o pkg autodiff
2973     autodiff_ini_model_io: comment out writing of grid information to netcdf
2974     files, because at this time the grid fields are a bunch of zeros
2975     (this is analogous to ini_mnc_vars.F)
2976 mlosch 1.1169 o pkg seaice/autodiff:
2977     left-over from removing the 3-time-level fields:
2978     - small rearrangement of common blocks (SEAICE.h)
2979     - fix field declaration in order to get meaningful output in
2980     adseaice.*.nc (adcommon.h)
2981 jmc 1.1165 o pkg obcs:
2982     - go through NH code only if nonHydrostatic=T
2983     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
2984 jmc 1.1174 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
2985 jmc 1.1166 => Update output of experiment seaice_obcs
2986     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
2987 jmc 1.1167 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
2988 jmc 1.1168 - fix restart for useOBCSprescribe + useEXF
2989 mlosch 1.1164 o pkg ctrl
2990     - make obcs as control parameter work also with useSingleCPUio
2991     - replace a few sny and snx by Ny and Nx to be consistent with
2992     ctrl_set_globfld_x/yz.F
2993 mlosch 1.1163 o pkg seaice
2994     - re-introduce global field frWtrAtm for the case of
2995     ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
2996     - catch the case of an empty filename in seaice_cost_init_fixed.F
2997     o pkg ecco:
2998     - small bug fixes in the_main_loop
2999     . fix order of monitor arguments
3000     . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
3001     . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
3002     that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
3003     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
3004     imbalance diagnostics for wmean_h/sflux = 0
3005     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
3006     - catch the case of empty filenames in ecco_cost_init_fixed.F
3007     and ecco_readparms.F
3008     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
3009 mlosch 1.1164 to make this statement meaningfull in ecco_cost_weights.F
3010 jmc 1.1162 o pkg zonal_filt:
3011     - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
3012     - when using rStar, filter uVel*hFacW instead of uVel
3013     (tested without topography: fix a Pb of growing instability with NLFS)
3014 dfer 1.1161 o pkg/aim/thsice:
3015     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
3016     (works as SST restoring)
3017 dfer 1.1160 o pkg/thsice:
3018     -add specific parameter for salt restoring in slab mixed-layer
3019     (by default equal to the temperature restoring)
3020    
3021 jmc 1.1203 checkpoint61v (2009/09/21)
3022 mlosch 1.1158 o pkg/kpp:
3023     -add double diffusive contributions as a hack, turned off by default
3024     for now, and the code can be excluded with a CPP-flag
3025     EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
3026     -add a verification experiments to "vermix" to test this code
3027 dfer 1.1157 o pkg/mom_common:
3028     Move computation of length scales to mom_init_fixed.F (avoid recomputation
3029     at each time-steps*levels).
3030 rpa 1.1156 o pkg/layers:
3031     Created a new package for computing volume fluxes in temperature or
3032     [not yet implemented] density layers, e.g. for calculating residual
3033     overturning circulations.
3034 jmc 1.1155 o pkg/diagnostics:
3035     implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
3036     o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
3037 jmc 1.1154 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
3038     To avoid mixing type (RS/RL) of input/output array argument,
3039     replace single mixed-type array with a pair from each type (RS/RL).
3040 jmc 1.1153 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
3041     is now implemented for all pkgs (previously only done for the main pickup)
3042    
3043 jmc 1.1203 checkpoint61u (2009/08/25)
3044 mlosch 1.1150 o pkg/obcs:
3045 mlosch 1.1151 - change OB?eta from _RS to _RL and put them into a separate commen block
3046     - add code to read OB?eta from a file via obcs_prescribe_read: the code
3047     compiles and does not destroy any other experiments, the data is read
3048     properly, but the code is not tested in actual applications
3049 mlosch 1.1149 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
3050     create a meaningful unit attribute for the time coordinate variable
3051 jmc 1.1148 o pkg/ebm: add plenty of missing "_d 0" ;
3052     update results of experiment global_ocean_ebm (fwd + adjoint tests)
3053     Notes: several pieces of code only works for (very) specific set up
3054     (domain size, lat range, etc ...); should be documented & stop if one
3055     of those assumptions is not meet.
3056 jmc 1.1147 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
3057     update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
3058     and offline_exf_seaice (seaicetd + adjoint).
3059 jmc 1.1146 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
3060     update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
3061     seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
3062     o few changes to pass when compiling with strick checking of arguments
3063     across S/R (allow to find few bugs in S/R calls).
3064 mlosch 1.1145 o pkg/seaice:
3065     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
3066     2d-fields, for slightly better performance
3067 jmc 1.1146
3068 jmc 1.1203 checkpoint61t (2009/07/22)
3069 mlosch 1.1142 o pkg/seaice:
3070     - remove unused variables in seaice_evp
3071     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
3072 jmc 1.1141 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
3073     named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
3074 jmc 1.1144 each processor opens a different file (a fix from Matt).
3075 jmc 1.1140 o cg2d:
3076     use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
3077     this reduces number of EXCH calls by 2 when using exch2.
3078     For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
3079     directives and missing simple EXCH (exch_s3d_rx) adjoint code.
3080     o pkg/thsice:
3081     add code for Near Infra-Red albedo (from Jeff)
3082 jmc 1.1139 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
3083 jmc 1.1140 o ini_model_io:
3084     move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
3085     MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
3086     to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
3087 jmc 1.1139
3088 jmc 1.1203 checkpoint61s (2009/06/30)
3089 jmc 1.1137 o pkg/exch2 (exch2_rxN_cube*):
3090     remove last BARRIER (no need to synchronise after getting data from shared
3091     buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
3092 jmc 1.1136 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
3093     and generate new output (for the 2 tests) using default rotationPeriod.
3094 jmc 1.1135 o pkg/exch2:
3095     - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
3096     (was already the case with AUTODIFF_EXCH2 defined)
3097     - add bj in exch2 arrays and S/R.
3098 jmc 1.1136 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
3099     MLAdjust to exch2 (identical results except with MPI -> truncation diff);
3100 jahn 1.1134 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
3101     - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
3102     GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
3103     - verification experiment natl_box.longstep
3104 jmc 1.1133 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
3105     allow different versions of ifort (8 or 9) and different versions
3106     of mpi (mpich or mpich2) to be used with the same optfile.
3107     requires to load a netcdf module and set MPI_INC_DIR (see comments inside
3108     optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
3109 jmc 1.1135 o pkg/seaice:
3110     fix previous modif (3-level field removed) for old-pickup reading
3111 jmc 1.1133
3112 jmc 1.1203 checkpoint61r (2009/06/25)
3113 mlosch 1.1129 o pkg/seaice:
3114 mlosch 1.1130 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
3115     1. introduce fields for time step (N-1)
3116     2. do not use levels 2 and 3 anymore (but keep them)
3117     3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
3118     includes changes to pkg/thsice/thsice_get_velocity.F,
3119     model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
3120     pkg/obcs/obcs_apply_uvice.F.
3121     - completely remove code for leap-frog time stepping for second order
3122 mlosch 1.1129 advection
3123 heimbach 1.1131 - adjusted adjoint accordingly;
3124     gradient checks have improved by an order of magnitude!
3125 mlosch 1.1130
3126 jmc 1.1203 checkpoint61q (2009/06/22)
3127 mlosch 1.1128 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
3128     - the boundary conditions along open boundaries are unclear, because the
3129     associated masks are set to zero and are thus treated as closed when
3130     applying the slip-boundary conditions.
3131     - move initialisation of grid variables from seaice_init_varia to _fixed
3132 dimitri 1.1127 o adding doc/diags_changes.txt
3133 jmc 1.1126 o model/src:
3134     do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
3135     to avoid "_diags" naming if no relation to pkg/diagnostics.
3136     ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
3137     file and only call PLOT_FIELD_XYZ if debugMode=T.
3138     remove few PLOT_FIELD_XY calls outside initialisation.
3139     remove few unnecessary BARRIER.
3140 dimitri 1.1125 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
3141     of salt_plume package in Southern Ocean
3142 jmc 1.1124 o pkg/thsice:
3143     - fix hOceMxL in overlap (needed for sea-ice advection);
3144     update output of experiment global_ocean.cs32x15.icedyn.
3145 mlosch 1.1123 o pkg/seaice:
3146     - make the (placeholder-)tracer IceAge a little more meaningful
3147 mlosch 1.1122 by avoiding ridging of age due to convergent ice flow
3148 dimitri 1.1127 - add diagnostics for surface temperature, atmospheric and oceanic
3149     heat flux, and atmospheric and oceanic ice growth
3150 mlosch 1.1122
3151 jmc 1.1203 checkpoint61p (2009/06/10)
3152 jmc 1.1120 o eesupp (global_max & global_sum):
3153     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
3154     - remove starting & endding barrier (no longer needed)
3155 jmc 1.1119 o pkg/mdsio, writelocal:
3156     works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
3157     (remove the STOP): uses shared buffer IO to store data from all threads
3158     and then let master-thread write nThreads tiles.
3159 jmc 1.1118 o pkg/mdsio (read/write field):
3160     - tiled IO done in 1 piece (all levels at a time);
3161 jmc 1.1119 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
3162 jmc 1.1118 - multi-threaded: allow to read/write local (non-shared) array
3163     (was already working with singleCpuIO ; now works also without);
3164     => no longer needs barrier call after reading a file (added inside
3165 jmc 1.1119 mds_read/write field).
3166 jmc 1.1118 - move barrier calls outside gather/scatter_2d to mds_read/write_field
3167 mlosch 1.1115 o pkg/obcs/exf
3168 mlosch 1.1116 - exf_getffieldrec.F: add a few ". _d 0" and
3169     add code to catch the case fldperiod = 0.
3170 mlosch 1.1115 - obcs_precribe_read.F: change if statements so that they match
3171     the variable type (_RL)
3172     - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
3173     exf_iprec) as part of namelist EXF_NML_01
3174 jmc 1.1114 o pkg/mdsio:
3175     - read/write tiled (local) files: read/write 1-level tile chunk at a time
3176     (instead of segment of length sNx); expected to speed up tiled IO.
3177     o pkg/exch2:
3178 jmc 1.1113 - take buffer copy from/to array out of S/R exch2_send/recv into new
3179     S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
3180     (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
3181     - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
3182 jmc 1.1114 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
3183 jmc 1.1113 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
3184     including Topology header file (and common blocks).
3185     - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
3186     remove 2nd exch call in exch2_s3d_rx (no longer needed).
3187     - document S/R arg. list (+ update some comments)
3188 dimitri 1.1117 o pkg/seaice:
3189     - added SEAICE_CLIM_AIR code, which permits modulation of surface air
3190     temperature and humidity over sea ice based on climatological values.
3191 mlosch 1.1111 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
3192     of LSR (this change is expected to change the results slightly because now
3193     it uses slightly difference moduli from the second last LSR solution, but
3194     that is more consistent with the stress computations; this part of the code
3195     is not tested in the verification experiments)
3196 mlosch 1.1110 - fix diagnostics for flux of ice in case of B-grid
3197     - turn strain rates eij and press into global fields within global
3198     common block in SEAICE.h for more straighforward diagnostics
3199     - fix diagnostics for principal stress components, press, zeta, eta
3200     to give something meaning full
3201 jmc 1.1109 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
3202     new output (all 4 tests) using default rotationPeriod.
3203 dfer 1.1112 o pkg KPP:
3204     - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
3205     - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
3206     and normal grid from 1 to Nr)
3207 dfer 1.1108 o Fix computations of L4rdt in mom_calc_visc.F
3208 jmc 1.1107 o eesupp:
3209     new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
3210     should be called before a "stop" if we know that all process are going
3211     to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
3212    
3213 jmc 1.1203 checkpoint61o (2009/05/26)
3214 jmc 1.1106 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
3215     o model/src/ini_curvilinear_grid.F:
3216 mlosch 1.1104 compute angleSin/CosC when they are not read from a file
3217 jmc 1.1106 o pkg/seaice:
3218 mlosch 1.1104 add pseudo time stepping for LSOR
3219 jmc 1.1103 o pkg/exch2:
3220     temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
3221 dimitri 1.1102 o pkg/seaice:
3222 dimitri 1.1105 Adding separate sea ice albedo, drag coefficients, and HO in Southern
3223     Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
3224 jmc 1.1101 o SingleCpuIO:
3225     fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
3226     o pkg/seaice:
3227 jmc 1.1100 put exchanged variable in (local) common block for MPI+Multi-Threads
3228     to work (necessary with exch1, and for now with exch2 too).
3229 jmc 1.1099 o verification: to get more experiments tested with mpi, mth and mpi+mth,
3230     change tiling of:
3231     aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
3232     hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
3233     update output of exp:
3234     exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
3235     tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
3236     + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
3237     (note: output.txt generated on faulks using only 1 tile)
3238 jmc 1.1098 o eesupp & mdsio (SingleCpuIO):
3239     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
3240     parameter "W2_useE2ioLayOut" (read from file "data.exch2").
3241     Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
3242     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
3243     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
3244     gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
3245 jmc 1.1097 o pkg/exch2:
3246     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
3247     read parameter file "data.exch2" if it exists; otherwise try default regular
3248     cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
3249     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
3250     with new code (not to be used, just as a backup solution).
3251 jmc 1.1098 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
3252     in utils/exch2/input.
3253 jmc 1.1097
3254 jmc 1.1203 checkpoint61n (2009/05/12)
3255 jmc 1.1095 o eesupp & mdsio (SingleCpuIO):
3256     - move mapping to global io-buffer inside gather_2d/scater_2d: this save
3257     memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
3258     receive real*4 array (instead of real*8) to read/write 32.bit files.
3259     (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
3260     and remove new mapping S/R)
3261 jmc 1.1094 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
3262     - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
3263     xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
3264     when using exch2. Add S/R to map global io-buffer to global model array.
3265     - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
3266    
3267 jmc 1.1203 checkpoint61m (2009/04/29)
3268 jmc 1.1094 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
3269     and add 3 other S/R for other types (R4,R8,RS).
3270 jmc 1.1092 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
3271     o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
3272     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
3273     - reduce number of macro definitions (keep only those which are used);
3274     can always call directly the corrresponding S/R if needed.
3275 jmc 1.1094 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
3276 jmc 1.1092 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
3277     Fixed wrong type of arg in:
3278 jmc 1.1094 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
3279 jmc 1.1092 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
3280     To fix: global_sum of var in common block is wrong (multi-threaded) in:
3281     dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
3282     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
3283 jmc 1.1094 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
3284     "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
3285 jmc 1.1091 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
3286     o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
3287     edges are closed (zero depth); might happen with "blank tiles";
3288 jmc 1.1094 for now, disabled if using OBCS.
3289 jmc 1.1091 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
3290 jmc 1.1090 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
3291 jmc 1.1091 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
3292 jmc 1.1089 to reduce length of 1.D array print in STDOUT.
3293 jmc 1.1088 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
3294     + use 48 tiles (16x8): this will allow to test "blank tiles".
3295     o start to test MPI + multi-threaded (change testreport to skip tests
3296     where number of tiles do not match).
3297     o genmake2: add option "-omp" to turn on Open-MP ;
3298     passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
3299 jmc 1.1086 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
3300     and keep the original tile numbering. Note: compatible with old
3301     W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
3302    
3303 jmc 1.1203 checkpoint61l (2009/04/07)
3304 jmc 1.1085 o Overlaps had been forgotten in calculating ijk keys : fixed
3305     o fix cyrus makedepend for gcc 4.4
3306 jmc 1.1084 o experiment fizhi-cs-aqualev20:
3307     switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
3308 jmc 1.1088 and generate new output. Note: new output is much closer to the old
3309     one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
3310 jmc 1.1084 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
3311     o pkg/fizhi:
3312     - change to avoid indices going deliberately over array-bounds
3313     - remove unnecessary MPI stuff
3314     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
3315     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
3316     does not go over array-bounds and therefore returns reliable output.
3317     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
3318     this S/R has 4 output arguments, which are used inside "get_alarm";
3319     when it is called with the same variable "ndum" in place of several
3320     output arguments, this produces weird side effect inside "get_alarm"
3321     (e.g., datein=dates(n) is overwritten by timein=times(n) since both
3322     datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
3323     address) and produces error.
3324 jmc 1.1090 o tools/gemake2: (March 27-29 2009)
3325     with option "-mpi": link *_mpi files from "MODS" dir (this is what
3326     testreport does).
3327 jmc 1.1083 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
3328 jmc 1.1084 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
3329 jmc 1.1083 update lab_sea.lsr & lab_sea.salt_plume results
3330 mlosch 1.1079 o pkg/seaice:
3331     Major overhaul of the LSOR solver: change discretization from original
3332     finite differences to finite volume. The old routine is still in the
3333     file seaice_lsr.F and can be turned on with the CPP-flag
3334     SEAICE_OLD_AND_BAD_DISCRETIZATION
3335     Along with this change, the discretization of the strain rates is changed.
3336     The same flag turns on the old discretization in seaice_calc_strainrates.F
3337     All verification experiments with seaice are affected (except for
3338     seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
3339     results by setting the above flag.
3340     Further changes involve changes in defaults:
3341     - ALLOW_FLOODING is defined and turned on by default
3342 heimbach 1.1087 - SEAICEadvSnow = .true. is now the default
3343     - SEAICEadvSalt = .true. is now the default
3344     - SEAICEadvAge = .true. is now the default
3345 mlosch 1.1081 - SEAICE_clipVelocities = .false. is now the default
3346     (as per J. Zhang's recommendation)
3347 mlosch 1.1079 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
3348     is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
3349     - seaice_growth: replace computation of UG by a simple copy from wspeed
3350    
3351 jmc 1.1203 checkpoint61k (2009/03/18)
3352 mlosch 1.1078 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
3353     seaice_lsr: fixed a few metric terms,
3354     affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
3355     add more debugging diagnostics
3356     seaice_evp: removed superfluous many metric terms of FV discretization
3357     of stress divergence
3358     affects lab_sea, lab_sea.hb87
3359     seaice_ocean_stress: removed superfluous many metric terms of FV discretization
3360     of stress divergence for non-evp solver
3361     (this part is not tested anywhere)
3362     seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
3363     they were effectively only half slip
3364     affects lab_sea.hb87
3365 jmc 1.1082 updated all relevant verification experiments (except lab_sea//output_adm.txt
3366     which was left over, but fails at level 7 & 6)
3367 mlosch 1.1078
3368 jmc 1.1203 checkpoint61j (2009/03/17)
3369 mlosch 1.1076 o pkg/seaice: turn a few hard wired parameters into run time parameters
3370 mlosch 1.1075 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
3371     time in seconds as promised by the usints in seaice_monitor and exf_monitor
3372 mlosch 1.1074 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
3373     that are not cubed-sphere grids
3374 mlosch 1.1073 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
3375 jmc 1.1072 o pkg/ctrl:
3376     fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
3377 jmc 1.1071 o non-hydrostatic (calc_gw.F):
3378     fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
3379     update output of exp. global_ocean.cs32x15.viscA4
3380     o remove backward compatibility for thetaMin,phiMin
3381 jmc 1.1070 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
3382 mlosch 1.1069 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
3383     interpolated wind field not only for curvilineargrid=.true., but also
3384     for a rotated grid (rotateGrid=.true.)
3385 mlosch 1.1068 o pkg/exf: add capability to bypass interpolation for runoff
3386     by setting yet another CPP-flag
3387 jmc 1.1070 o eesupp/src, B-grid exchange:
3388     add simple (6 tiles, non MPI) CS exch + standard interface S/R.
3389 heimbach 1.1067 o autodiff
3390     new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
3391     allows to switch to single-prec common blocks;
3392     corresponding switch occurs in tamc.h, integer isbyte
3393     TAF store directivs "byte" and "kind" seem equivalent;
3394     Most tamc.h have been updated correspondingly.
3395    
3396 jmc 1.1203 checkpoint61i (2009/02/13)
3397 heimbach 1.1066 o autodiff:
3398     fix autodiff_sore/_restore indices for obcs
3399     (spotted by I. Hoteit, M. Mazloff)
3400 heimbach 1.1065 o pkg/autodiff, pkg/ctrl:
3401     Add flag to reduce all tapelev I/O to single-prec.
3402     In data.ctrl set
3403     doSinglePrecTapelev = .TRUE.
3404 jmc 1.1070 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
3405     check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
3406 mlosch 1.1062 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
3407     real fresh water flux (not yet)
3408 jmc 1.1060 o pkg/mdsio & rw:
3409     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
3410     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
3411 jmc 1.1058 o pkg/flt:
3412     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
3413     init_fixed & ini_varia.
3414 jmc 1.1059 - clean-up & simplify linear interpolation S/R:
3415     move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
3416     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
3417 jmc 1.1060 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
3418 jmc 1.1061 - add vert. coordinate & horiz. indices to output files.
3419     - change vertical position in initial condition, from index to depth [m].
3420 jmc 1.1063 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
3421     (easier to get to a curvilinear grid) ; delX,delY no longer used.
3422 dfer 1.1057 o pkg/ggl90: a few modifications:
3423     - fix bottom boundary condition, and interpolation of KappaE
3424     near top and bottom
3425     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
3426     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
3427     - add a few options for mixing-length upper limit (--> mxlMaxFlag)
3428 jmc 1.1056 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
3429     (maintain temporary backward compatibility, until next checkpoint)
3430    
3431 jmc 1.1203 checkpoint61h (2009/01/27)
3432 jmc 1.1054 o pkg/diagnostics with "periodic averaging diagnostics":
3433     fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
3434 jmc 1.1053 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
3435 mlosch 1.1052 o pkg/obcs: fix loop ranges for balancing code
3436 jmc 1.1051 o pkg/flt:
3437     - improve criteria for finding which tile owns a float.
3438     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
3439 dfer 1.1050 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
3440     aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
3441     with ocean biogeo)
3442 jmc 1.1049 o pkg/flt:
3443     - do some cleaning and fix the restart ;
3444     - add output.txt in flt_example/results to get this pkg tested.
3445     o genmake2: add an EXTENDED_SRC option and flag.
3446     for now, cannot be turned on on command line (only through genmake_local)
3447 jmc 1.1048 o pkg/mdsio: read/write vector:
3448     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
3449 jmc 1.1049 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
3450 jmc 1.1048 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
3451     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
3452     (drop to 4 digits matching for grad). But this test does not look very
3453     reliable (was already failling on eddy, fc5, at 6.digits). Update output.
3454    
3455 jmc 1.1203 checkpoint61g (2008/12/29)
3456 jmc 1.1046 o pkg/flt:
3457     - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
3458     + make OPTIONS file more standard.
3459     - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
3460     - fix _BYTESWAPIO CPP-Flag
3461     - standard reading of file-parameter "data.flt"
3462 jmc 1.1047 - fix argument list of S/R FLT_RESTART
3463 jmc 1.1046 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
3464 mlosch 1.1045 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
3465 mlosch 1.1044 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
3466     a still unfixed compiler/optimization bug
3467    
3468 jmc 1.1203 checkpoint61f (2008/11/21)
3469 jmc 1.1042 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
3470     update results of global_ocean.cs32x15.icedyn test.
3471 jmc 1.1041 o move getcon.F from model/src to pkg/fizhi.
3472 jmc 1.1040 o pkg/exf: add parameter for extrapolation of temp up to the surface
3473     and option to prevent negative evap (in bulk_largeyeager04 only).
3474 jmc 1.1039 o Prather Advection scheme: fix tracer conservation for divergent flow
3475     (e.g., when using NonLin Free-Surface).
3476 dfer 1.1038 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
3477 jmc 1.1037 o gmredi (Visbeck-variable-K):
3478     - add more parameters to Visbeck-variable-K.
3479     - use a 5 points average for dSigmaR in Visbeck-K calculation
3480     (more "homogenous": same stencil and same weights as in dSigmaH)
3481     - update output of ideal_2D_oce experiment.
3482 mlosch 1.1034 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
3483     (#undef REAL4_IS_SLOW)
3484     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
3485     coordinate variable
3486     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
3487     (surface forcing fields), removes some of the functionality
3488     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
3489     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
3490     probably not all: copy _RS surface flux fields to RL field before
3491     calling DIAGNOSTICS_FILL
3492 mlosch 1.1035 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
3493     real*4 (CALL EXCH_*_RS) versions.
3494 jmc 1.1036 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
3495     (generate new output).
3496 mlosch 1.1034
3497 jmc 1.1203 checkpoint61e (2008/10/23)
3498 jmc 1.1032 o gmredi (Visbeck-variable-K):
3499     - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
3500     - change computation of Visbeck-K where Slope > Smax :
3501     now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
3502     previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
3503 jmc 1.1031 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
3504     to be the same as with Z-coord. (i.e., m/s & no-units respectively).
3505     o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
3506 jmc 1.1030 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
3507 jmc 1.1032 does not become too large (to avoid precision problems in implicit-diffusion
3508 jmc 1.1030 solver); update ideal_2D_oce output.
3509 dfer 1.1028 o pkg ggl90:
3510     - in ggl90_cal.F: compute only one set of visc/diff, used to
3511     step forward TKE/T/S/momentum
3512     - default value of GGL90viscMax/GGL90diffMax larger and equal (to
3513     have Prandlt =1)
3514 jmc 1.1032 o gmredi (fm07):
3515 jmc 1.1029 - add lower limit on Transition layer thickness + lower limit on 1/lambda
3516 jmc 1.1027 - allow to set few more params from data.gmredi
3517 dfer 1.1026 o pkg ggl90:
3518     - add missing sqrt(2) factor in computation of mixing length
3519     scale in ggl90_calc.F
3520     (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
3521    
3522 jmc 1.1203 checkpoint61d (2008/09/25)
3523 heimbach 1.1025 o adjoint modifs
3524     - adapt to new field rhoInSitu
3525     - allow to revert from StoreDynVars2D, StoreDynVars3D
3526     to individual fields
3527     (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
3528 jmc 1.1024 o store 3-D (in-situ) density in commom block (DYNVARS.h)
3529     - save 1 rho computation.
3530     - no longer modify T & S inland when using down_slope pkg.
3531 jmc 1.1023 o gad_som : allow to switch to SOM advection for T & S without corresponding
3532     pickup files (using new S/R: MDS_CHECK4FILE).
3533     o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
3534     (for useSingleCpuIO to work in multi-threaded)
3535 mlosch 1.1022 o pkg/shelfice:
3536     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
3537     with SHELFICEtopoFile in data.shelfice
3538     - move code for reading ice shelf topography and modifying hFacC into separate
3539     subroutines of the shelfice package
3540     - separate initialisation of "fixed" and "variable" variables
3541     - kTopC is not (yet) replaced by kSurfC, although this is possible
3542 jmc 1.1023 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
3543 jmc 1.1020 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
3544     and rename:
3545     ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
3546     ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
3547     o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
3548    
3549 jmc 1.1203 checkpoint61c (2008/08/30)
3550 jmc 1.1018 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
3551     to add mass source/sink of fluid in the interior (3-D generalisation
3552     of oceanic real-fresh water flux).
3553     o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
3554 jmc 1.1017 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
3555 jmc 1.1016 o new pkg: down_slope
3556     density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
3557     - presently, modify T & S inland (dwnslp_calc_rho.F).
3558     can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
3559     - implementation for ocean in P-coords not tested.
3560     - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
3561     o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
3562 jmc 1.1015 (to facilitate conversion of oceanic pkg to p-coordinate).
3563 jmc 1.1014 o change FIND_RHO to FIND_RHO_2D :
3564     pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
3565     o new pkg: cheapaml
3566    
3567 jmc 1.1203 checkpoint61b (2008/08/05)
3568 jmc 1.1011 o exch2:
3569 jmc 1.1012 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
3570     - no longer depend on the order sequence (N,S,E,W).
3571     - 3rd exchange no longer needed (tested with 24 tiles).
3572     - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
3573     - exch_UV_A-grid readily available (but not yet tested).
3574     comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
3575     (both are no longer needed) in exch_uv: no effect in forward run; but
3576     get truncation error differences with adjoint exch.
3577     o exch2:
3578 jmc 1.1011 - change index-bounds storage (moved from target to local tile,
3579     more intuitive this way) ; rename/remove some variables.
3580 jmc 1.1012 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
3581 jmc 1.1011
3582 jmc 1.1203 checkpoint61a (2008/07/29)
3583 jmc 1.1009 o exch2/matlab-topology-generator:
3584     fix bug in index bounds for N-S internal exchange (hard to tell if this
3585     had any effect on the solution).
3586 mlosch 1.1008 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
3587     is exceeded
3588 mlosch 1.1007 o testreport: modify syntax of awk, so that it works also with
3589     awk, and not only with nawk and gawk
3590    
3591 jmc 1.1203 checkpoint61 (2008/06/24)
3592 heimbach 1.1005 o autodiff
3593     Change default for TAF usage by removing argument '-nonew_arg'
3594     This changes TAF subroutine argument list (ordering of active var.)
3595     Omission of this flag leads to incompatibility w.r.t. TAMC
3596     To restore TAMC-compatibility, need following modifs:
3597     * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
3598     * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
3599     Tested TAF version is 1.9.22
3600     N.B.: exch2 hand-written adjoint code currently not TAMC compatible
3601    
3602 jmc 1.1203 checkpoint60 (2008/06/19)
3603 heimbach 1.1004 --->>> This is the last checkpoint for which generating the adjoint
3604     --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
3605     --->>> by default.
3606     --->>> Future checkpoints will ommit this flag by default.
3607 jmc 1.1003 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
3608 gforget 1.1002 o pkg/grdchk: Add gradient check to etan0 perturbations.
3609 gforget 1.1001 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
3610 gforget 1.1000 o pkg/autodiff: more flexibility in zeroadj.
3611     model/src: modifying do_oceanic_phys.F accordingly.
3612 gforget 1.999 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
3613     o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
3614     special setup of gmredi for which the adjoint is stable
3615     enough for parameter optimization.
3616 gforget 1.998 o bridging the gap between eddy stress and GM.
3617     -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
3618     along with a change in CPP option (now ALLOW_EDDYPSI).
3619     -> when using GM w/ GM_AdvForm:
3620     The total eddy streamfunction (Psi = eddyPsi + K x Slope)
3621     is applied either in the tracer Eq. or in momentum Eq.
3622     depending on data.gmredi (intro. GM_InMomAsStress).
3623     -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
3624     The key modifications are in model/src/taueddy_external_forcing.F
3625     pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
3626 jmc 1.1003
3627 jmc 1.1203 checkpoint59r (2008/05/29)
3628 jmc 1.996 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
3629     from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
3630     fix option to read coriolis(@ cell-corner) from files with CS-grid.
3631 mlosch 1.995 o pkg/mnc: add some attributes to standard 1D-coordinate variables
3632 mlosch 1.993 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
3633     mass points, when using mnc for output
3634     - add runtime parameter (missing_value, missing_value_int) to override
3635     default (which is the value of getcon('UNDEF'))
3636     o pkg/mnc: prepare mnc for the actual use of missing values with the
3637     diagnostics package: small fix in mnc_cw_readwrite.template and more
3638     initialisation of never used fields
3639 mlosch 1.994 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
3640     versions
3641     o pkg/thsice/thsice_ini_vars.F added default initial values so that
3642     thermodynamics sea ice solver does not blow up when some initial fields
3643     are missing.
3644 jmc 1.991 o move from external_forcing_surf.F to ini_forcing.F
3645     the p-coord. hack consisting in using pLoad to set phi0surf ;
3646     update output of tutorial_global_oce_in_p (affected @ truncation level).
3647 dfer 1.990 o Freshen up a bit hs94.1x64x5, notably:
3648 mlosch 1.994 remove rotationPeriod and tRef=5*0. (adjoint only), and add
3649     exactConserv=.TRUE.
3650 jmc 1.989 o pkg/generic_advdiff:
3651     change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
3652     applies to files where Temperature & Salinity 2nd Order moments are used.
3653 jahn 1.988 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
3654     this uses a dynamically allocated internal state data structure
3655     (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
3656     and requires a fortran 90 compiler
3657    
3658 jmc 1.1203 checkpoint59q (2008/05/06)
3659 jmc 1.986 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
3660     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
3661 dfer 1.985 o Refresh tutorial_global_oce_biogeo, notably:
3662     - change bathymetry (put back seamounts in ACC, use hFacs)
3663     - change EOS (POLY3 --> JMD95Z)
3664     - use Bryan-Lewis vertical diffusivity
3665     - use multidimensional advection
3666     - remove old virtual virtual in dic pkg, now done through ptracer pkg
3667     - change a couple of parameters in dic pkg
3668 gforget 1.984 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
3669 mlosch 1.982 o pkg/obcs: change default to OBCSfixTopo = .true.,
3670 mlosch 1.983 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
3671     - replace "debugMode" with "debugLevel .GE. debLevB"
3672 gforget 1.981 o implementation of TAF directives for gchem,cfc,dic
3673 jmc 1.980 o remove "exp5" (replaced by tutorial_deep_convection).
3674 mlosch 1.979 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
3675     this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
3676     the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
3677 mlosch 1.982 --> changes results in exp4, seaice_obcs
3678 jmc 1.980 o tutorial_deep_convection :
3679 jmc 1.978 update the set-up and increase resolution and domain size ; start
3680     from pseudo initial conditions = output at t=120mn in order to see
3681     something happening when running testreport.
3682 mlosch 1.976 o pkg/seaice: add os7mp as an advection scheme
3683     add check for advection schemes
3684 mlosch 1.977 add a flag for restoring T and S underneath sea ice
3685 mlosch 1.975 o pkg/my82: add netcdf-support and diagnostics
3686 dfer 1.974 o thsice pkg:
3687 mlosch 1.979 - Now hsMax limits snow height by turning it into ice following
3688 dfer 1.974 flooding scheme (and now conserving energy)
3689     - Slight rewriting of the formula in thsice_calc_thick.F
3690     - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
3691 jmc 1.980 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
3692 dfer 1.974
3693 jmc 1.1203 checkpoint59p (2008/04/10)
3694 jmc 1.973 o gchem / dic / cfc :
3695     - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
3696     - add new parameter files: "data.dic" & "data.cfc" ;
3697     - various re-arrangement in initialisation & header file ;
3698     - fix tutorial_global_oce_biogeo for multi-threaded test.
3699     o pkg/dic: test for "pickup_dic" file when restarting ;
3700     if no pickup-file, can restart with a re-initialised pH (same as it did
3701 jmc 1.972 before) providing pickupStrictlyMatch is set to False.
3702 jmc 1.971 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
3703     + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
3704 jmc 1.970 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
3705     and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
3706     o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
3707     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
3708     (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
3709 jmc 1.969 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
3710     scheme to use for vorticty-term ;
3711     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
3712     (with default selectVortScheme, return to original discretisation)
3713     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
3714 mlosch 1.968 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
3715 jmc 1.967 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
3716     bottom ; only used with variable horizontal viscosity and non-hydrostatic.
3717     also fix diagnostics VISCAHW & VISCA4W.
3718    
3719 jmc 1.1203 checkpoint59o (2008/03/07)
3720 jmc 1.965 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
3721 mlosch 1.964 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
3722     move a few statemens out the main loop into separate loops
3723 mlosch 1.962 o pkg/shelfice:
3724     - sort out freshwater flux; convert freshwater fluxes to mass fluxes
3725     (kg/m^2/s), does not break tests, because in verification/isomip,
3726     rhoConstFresh=rhoConst (by accident)
3727 mlosch 1.963 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
3728     - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
3729     new file model/src/seawater.F, so that they are available for all pkgs.
3730     - convert potential temperature into in-situ temperature. This changes the
3731     isomip tests => update tests
3732 mlosch 1.961 o add a flag writePickupAtEnd (default=true) to be able to suppress
3733     writing a pickup at the last timestep
3734 jmc 1.966 o tools/mpack-1.6 :
3735     - disable automake (not working) and autoconf (not needed).
3736     - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
3737     also cleaner with much less compilation warnings.
3738 gforget 1.960 o pkg/profiles:
3739     rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
3740     (for "less than 32 characters name" compiler requirement)
3741 dimitri 1.959 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
3742     conditions that have a different sampling frequency than S/T/U/V obcs
3743 jmc 1.958 o pkg/diagnostics (stats-diags):
3744     - fix global Min/Max in case 1 processor get only empty tiles
3745 mlosch 1.957 o genmake2: replace (4 times)
3746     make genmake_tc_1.o >> genmake_warnings 2>&1
3747     with
3748     COMM="$CC $CFLAGS -c genmake_tc_1.c"
3749     echo $COMM >> genmake_warnings
3750     $COMM >> genmake_warnings 2>&1
3751     to make genmake2 always see the value of CC as specified in the optfile.
3752 jmc 1.956 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
3753     - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
3754     - modify verification advect_cs test to test SOM-advection on CS-grid.
3755 gforget 1.955 o pkg/ctrl:
3756     - Rewrite of ctrl_map_ini_ecco.F,
3757     introducing a generic routine (ctrl_map_ini_gen.F).
3758     - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
3759 jmc 1.956
3760 jmc 1.1203 checkpoint59n (2008/02/09)
3761 jmc 1.953 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
3762     number in dedicate array "hdiag":
3763     - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
3764     with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
3765     - many small changes (integer format) for large number of diagnostics
3766     - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
3767     a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
3768 mlosch 1.952 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
3769     usingSphericalGrid, this allows to define the rotated grid coordinates
3770     via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
3771     geographical coordinates according to the inverse of the rotation defined
3772     by the Euler angles, so that Coriolis parameter and online-interpolation by
3773     exf works with the geographical coordinates on XC/YC/XG/YG.
3774     Naturally, this feature does not work with all packages, so some
3775     combinations are prohibited in config_summary (flt, flt_zonal, ecco,
3776     profiles), because there the coordinates are assumed to be regular
3777     spherical grid coordinates.
3778 gforget 1.951 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
3779     - introduce isopycnal diffusion coefficient control.
3780     o tools/adjoint_options:
3781     - additional control vector components.
3782 mlosch 1.950 o pkg/mnc: have mnc create marginally meaning full coordinate variables
3783     (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
3784 jmc 1.948 o pkg/mypackage:
3785     - add example of read/write pickup for state-var ;
3786     - add entry points to the main code for state-vars diags & write-pickup.
3787 dimitri 1.946 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
3788     transitions for useExfYearlyFields
3789 mlosch 1.947 - add new subroutine that determines the file to read from for
3790     use*YearlyFields = .TRUE. and .FALSE.
3791 mlosch 1.949 - add a verification experiment to global_with_exf that tests
3792     useExfYearlyFields with USE_EXF_INTERPOLATION defined
3793 mlosch 1.945 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
3794     analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
3795     subroutines (which could be generated from a template, because they are
3796     almost identical), for now they are included in obcs_prescribe_read.F for
3797     simplicity
3798 mlosch 1.943 o pkg/exf:
3799     - add a little more diagnostic to exf_interp_read (in analogy to
3800     mds_read_field, can be turned off with debugLevel < debugLevA=1)
3801     - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
3802 mlosch 1.944 ugly but fast by unrolling short inner loops, inserting a unroll=8
3803     directive in routine lagran, and splitting a loop and making do while the
3804     outermost loop (the latter requires the intoduction of index arrays)
3805 dimitri 1.942 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
3806 dimitri 1.941 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
3807     http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
3808 dimitri 1.940 o verification/seaice_obcs: updated for restart test and latest options
3809 mlosch 1.939 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
3810     ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
3811     for now this is only available for the C-grid code and also within
3812     #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
3813    
3814 jmc 1.1203 checkpoint59m (2008/01/14)
3815 dimitri 1.936 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
3816     and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
3817 dimitri 1.937 o gad_som : fix flux output (& diagnostics) to have same units as other
3818     advection scheme fluxes (was previously multiplied by deltaT).
3819 dimitri 1.933 o added verification/seaice_obcs both to test seaice open boundaries
3820     and to provide an example matlab scrpt for generating them
3821     o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
3822 atn 1.931 o pkg/salt_plume: clean up salt_plume_frac.F to
3823     remove redundancy in PlumeMethod 1 and 4
3824 atn 1.930 o pkg/kpp: added saltplume diagnostics
3825 dimitri 1.929 o pkg/obcs and pkg/seaice:
3826     - do not set uice and vice to zero when OB*icefile are unspecified
3827     - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
3828     - moved seaice tracer obcs after call to seaice_growth
3829 dimitri 1.927 o pkg/salt_plume: added various options for salt plume depth
3830     criterion and for vertical distribution of the salt
3831 jmc 1.928
3832 jmc 1.1203 checkpoint59l (2007/12/18)
3833 jmc 1.925 o pkg/ptracers: new version of ptracers pickup:
3834     read meta file and write only fields which are needed to restart.
3835     ( same logic as main pickup file ; also using pickupStrictlyMatch )
3836 dimitri 1.924 o pkg/seaice:
3837 mlosch 1.923 - add timescale for melting due to warm mixed layer as a means of
3838     setting SEAICE_availHeatFrac more conveniently
3839     - add a CPP-flag/runtime parameter check for flooding algorithm
3840 dimitri 1.924 - reformulated availHeat in seaice_growth.F to be independent of AREA
3841 mlosch 1.923 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
3842     unit changes
3843 dimitri 1.921 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
3844 mlosch 1.919 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
3845     SX vector computer.
3846 dimitri 1.920 o pkg/seaice:
3847     - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
3848     seaice forcing fields can now be read only through pkg/exf
3849     - removed some unused halos
3850 jmc 1.917 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
3851 dimitri 1.922 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
3852     or U/VICE from U/VWIND before computing U/VSTRESS
3853 dimitri 1.916
3854 jmc 1.1203 checkpoint59k (2007/11/30)
3855 dimitri 1.914 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
3856     dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
3857 jmc 1.913 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
3858 jmc 1.925 all experiments pass when compile with un-initialised var. checking option.
3859 dimitri 1.912 o added pkg/salt_plume
3860 jmc 1.911 o script to test restart (for now, in MITgcm_contrib/jmc_script)
3861     o pkg/seaice: new read/write pickup version.
3862     read meta file and write only fields which are needed to restart.
3863     ( same logic as main pickup file ; also using pickupStrictlyMatch )
3864 mlosch 1.910 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
3865 jmc 1.909 o lab_sea.hb87: modify the domain & update output.hb87.txt :
3866     lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
3867     at j=1 & j=Ny+1 : this case is not treated correctly in the restart
3868     process. Fixed here by closing the domain at the Northern boundary.
3869     o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
3870     o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
3871     a set of consecutive levels in/from a 3-D array.
3872 jmc 1.908 o pkg/ptracers:
3873 jmc 1.909 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
3874 jmc 1.908 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
3875    
3876 jmc 1.1203 checkpoint59j (2007/11/09)
3877 jmc 1.906 o in pkgs: dic, obcs, offline, rbcs:
3878     standard way to compute coeff. for time interpolation between 2 time reccords
3879     which retains full precision (& make results less dependent on compiler).
3880     update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
3881 mlosch 1.905 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
3882     packages instead of reading ice cover and wind speed separately
3883 jmc 1.904 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
3884     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
3885     to allow to compile customized code before the update)
3886 jmc 1.903 o cleaning-up:
3887     - fix CPP instruction syntax in pkg/obcs
3888     - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
3889     add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
3890     - fix some threads issue in IO parts.
3891 dfer 1.901 o pkg/dic:
3892     - add tons of "_d 0" (--> much better testreports !)
3893     and then update outputs of tutorial_global_oce_biogeo
3894 jmc 1.900 o pkg/mom_fluxform:
3895     add a special version of momentum advection intended to conserve momentum
3896     next to a bathymetry step or a coastline edge. (default = off = #undef)
3897 jmc 1.898 o new read/write pickup version:
3898     - for now, only implemented for main (mdsio) pickup file.
3899     - write out only what is needed to restart; merge pickup_nh , pickup_ph
3900     and main pickup together.
3901     - read meta file; read only what is needed to restart; stop if a field
3902     is missing (if pickupStrictlyMatch=T, = the default) or try to restart
3903     if it make sense (even if the restart is not perfect).
3904     - if no meta file, assume that pickup to read corresponds exactly to
3905     a pickup that would currently be written.
3906     - read pickup written in the old format (until checkpoint59i) if it
3907     recognizes an old meta file (no field-list).
3908     - add a meta file in exp. which starts from a pickup: 2 cases:
3909     a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
3910     e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
3911     b) a meta file describing the content of the associated pickup file
3912     e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
3913     o pkg/mdsio & pkg/rw:
3914     - new routine to read a meta file ; new set of routine to read
3915     Multiple-fields file (with meta file).
3916 dimitri 1.899 o added open boundary conditions capability for seaice
3917     HSNOW, HSALT, UICE, and VICE
3918 dimitri 1.897
3919 jmc 1.1203 checkpoint59i (2007/10/21)
3920 heimbach 1.895 o adjoint:
3921     * fix multiDimAdvection adjoint
3922     (partial recomputation problem by TAF for fVerT(:,:,kDown)
3923     and comlev1 size definition (maxpass vs. max. number of tracers)
3924     * verification/global_ocean.90x45x15 adjoint now tests
3925     NLFS and multiDimAdvection using DST3 (=30)
3926     * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
3927 jmc 1.894 o pkg/kpp: add "_d 0" to real constant (if missing);
3928     update output of exp: natl_box (10.digits); vermix (std, 7.digits)
3929     and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
3930 jmc 1.893 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
3931     for internal parameters related to restart process (formerly from PARAMS.h)
3932     and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
3933     o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
3934     as argument. (only atm2d & obcs write_pickup have not yet been updated)
3935 jmc 1.892 o pkg/monitor:
3936     - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
3937     - fix mon_stats_rs (statistics over the full domain, even where field is zero)
3938     - account for deep Atmosphere factor and density factor (anelastic)
3939 dimitri 1.891 o added open boundary conditions capability for seaice HEFF and AREA
3940 mlosch 1.890 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
3941     thermodynamics
3942     - requires a little reorganization, which affects the testreport results
3943     of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
3944     so that now the conservative form is tested
3945     - add a few comments
3946 jmc 1.892 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
3947 mlosch 1.888 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
3948 mlosch 1.887 o add new diagnostics to seaice: advective, diffusive fluxes (only for
3949     multidim-advection, for scheme 2 they are not filled) and transports,
3950     thermodynamic growth rates
3951 jmc 1.902 o change units of EmPmR (inside the code, + within coupling interface)
3952     from m/s to kg/m2/s (mass flux) but leave input file unchanged.
3953     Affects results @ truncation level (cg2d match) and update output of
3954     experiments: lab_sea(6), global_ocean.90x40x15(10),
3955 jmc 1.886 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
3956     + adjoint results: global_ocean_ebm(11) and lab_sea (12).
3957 jmc 1.902 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
3958 jmc 1.886 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
3959    
3960 jmc 1.1203 checkpoint59h (2007/09/29)
3961 mlosch 1.884 o pkg/exf:
3962     - improve vectorization by moving if-statement out of loops in
3963     exf_mapfields, exf_radiation
3964     - exf_bulkformulae.F: introduce 2D fields and vectorize code
3965 dimitri 1.881 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
3966 jmc 1.880 o testreport:
3967     - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
3968     monitor & update offline_exf_seaice exp. output.
3969     - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
3970 mlosch 1.879 o pkg/seaice:
3971     - bug fix in the evp solver: boundary conditions were affected be
3972     masking of zMax/zMin (changes results)
3973     - minor bug fix in boundary conditions in seaice_calc_strainrates
3974     (changes results for no_slip)
3975     - seaice_lsr.F: make interpolation of eta dependent on boundaries
3976     - replace hardcoded lower limit for zeta (zMin) by runtime parameter
3977     - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
3978     stress formulation and no-slip boundary conditions
3979 jmc 1.878 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
3980     in gad_calc_rhs.F ; add few safety stops in initialisation phase.
3981 dimitri 1.877 o pkg/seaice: a first HSALT time stepping equation has been checked in
3982 dimitri 1.875 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
3983     in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
3984     without requiring DO-IF statements
3985 jmc 1.876 o pkg/thsice:
3986     use continuous power-law function for partition of energy between lateral
3987     melting/freezing and thinning/thickening ; old code using step function
3988     still available with #undef THSICE_FRACEN_POWERLAW
3989     update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
3990     o testreport: change AD testing : check against results/output_adm.txt
3991     using same scripts as for forward test.
3992 dimitri 1.875
3993 jmc 1.1203 checkpoint59g (2007/09/17)
3994 jmc 1.873 o adjoint testing: in preparation for changing testreport:
3995     - output format: cost and grad written on separated lines
3996     - ad output results in directory "results" (instead of "results_ad")
3997 dimitri 1.872 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
3998 dimitri 1.871 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
3999 gforget 1.870 o pkg/ecco: allow user defined cost function contributions
4000 jmc 1.869 o testreport:
4001     Allow to choose (per experiment) the list of tested output variables
4002     and the main variable (used to issue a pass/FAIL ) ;
4003     - for now, done by adding the specific list in file: [exp]/input/tr_checklist
4004 jmc 1.873 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
4005 jmc 1.869 Also modify printing of summary:
4006     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
4007     b) echo the list of tested variables in the individual summary.txt of
4008     each experiment.
4009 jmc 1.868 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
4010     threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
4011     (but still depend on the tile decompostion of the domain).
4012 mlosch 1.867 o pkg/seaice: change a discretization detail to make the B-grid code
4013     "more symmetric". This change is likely to remove all "ridges/leads" that
4014     where quasi-aligned with the grid in B-grid solutions. It may also be
4015     the solution to the stress coupling issues with the B-grid.
4016 jmc 1.866 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
4017     remove .cvsignore from input dir. (since testreport no longer run here).
4018 jmc 1.865 o pkg/thsice:
4019 jmc 1.866 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
4020 jmc 1.865 - fix reshaping of sea-ice just after advection:
4021     melt all the ice only if ice-volume is too small.
4022     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
4023     prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
4024     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
4025 jmc 1.864 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
4026     tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
4027 jmc 1.863 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
4028     forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
4029     (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
4030     and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
4031     of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
4032     -> update output.txt
4033     o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
4034     this affects truncation error: -> update output.txt of exp:
4035     global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
4036     ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
4037    
4038 jmc 1.1203 checkpoint59f (2007/08/21)
4039 gforget 1.861 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
4040     o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
4041     a bounded range (in forward mode)
4042 gforget 1.860 o pkg/ecco, ctrl, autodiff and mom_common:
4043     internal parameter controls, completements of implementations
4044 jmc 1.859 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
4045 jmc 1.862 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
4046     (not seem any difference in testing results).
4047 jmc 1.859 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
4048     at face corners.
4049 jmc 1.858 o pkg/generic_advdiff:
4050     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
4051     loop range indices for computing vertical advection tendency
4052     and do the calculation in the interior only (no overlap) ;
4053     for now, only implemented for SOM advection (to save CPU time).
4054     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
4055 heimbach 1.855 o exch2 adjoint
4056     First set of changes:
4057     - add exch2 hand-written adjoint templates
4058     - exch2 hand-written no longer use TAF-flag 'nownew_arg'
4059     This will require cleanup in pkg/autodiff/*.F
4060     (changed routines currently kept separate in verif. code/)
4061     - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
4062     that used to hide exch2 or cubed-sphere specific code
4063     (commented via 'cph-exch2')
4064 dimitri 1.856 o pkg/seaice
4065     - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
4066 jmc 1.857 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
4067     output of global_ocean.cs32x15.thsice .
4068 heimbach 1.855
4069 jmc 1.1203 checkpoint59e (2007/07/26)
4070 jmc 1.853 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
4071     for B-grid vector (not yet tested) and C-grid vector (<- only used
4072     when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
4073 dimitri 1.852 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
4074     (#ifdef ALLOW_SALT_PLUME)
4075 dimitri 1.851 o gather_2d/scatter_2d: removed halo regions
4076 jmc 1.845 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
4077     scheme and the corresponding test case (under front_relax dir). For now,
4078     only available with Skew-flux form and not yet tested in realistic set-up.
4079 heimbach 1.847 adjoint: store directives updated, but gradient checks deteriorated,
4080     so maybe GM/Redi adjoint is now broken.
4081 heimbach 1.844 o seaice adjoint
4082     * add AREA, HEFF, HSNOW as control variable
4083     (should not change lab_sea results)
4084     * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
4085 dimitri 1.848 o pkg/seaice:
4086     * added computation of saltFlux in seaice_growth;
4087     For time being, sea ice salinity is assumed constant
4088     contribution of snow flooding to freshening of sea ice is neglected.
4089     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
4090     defaults to 0.0 in order to maintain backward compatibility.
4091     Typical values for SEAICE_salinity are 4 to 10 g/kg.
4092     * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
4093     * added SEAICE_availHeatFrac, which specifies fraction of surface level
4094     heat content used to melt or grow ice
4095 dimitri 1.849 * commented out cap of HICE: it helps keep ice thinner
4096     * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
4097 dimitri 1.850 * applied OBCS T/S mask to HEFFM sea ice mask
4098 heimbach 1.844
4099 jmc 1.1203 checkpoint59d (2007/06/21)
4100 jmc 1.842 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
4101     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
4102     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
4103     o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
4104     and change default value of parameter "GM_Small_Number";
4105     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
4106     global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
4107     tutorial_global_oce_biogeo, tutorial_global_oce_latlon
4108 gforget 1.841 o pkg/ecco: cost function when applying pkg/smooth to controls
4109     o pkg/ctrl: add forcingPrecond run time parameter
4110 mlosch 1.839 o pkg/seaice:
4111     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
4112     - fix bug in metric terms of u-equation in LSR solver (implicit part),
4113     changes verification/lab_sea
4114     - rearrange implicit part of u-equation in LSR solver to make it easier to
4115     read, understand, and debug. This causes changes at the truncation level.
4116     - fix (serious) bug in the boundary conditions (sign error in the implicit
4117     part) of the LSR solver. Changes all LSR results.
4118 dimitri 1.840 - fixed problem with HSNOW initialization to avoid thick snow when AREA
4119     is initilized with small values - does not change lab_sea results.
4120     - added HsnowFile initialization capability
4121 gforget 1.838 o pkg/smooth: addition to model/src and pkg/ctrl so allow
4122     initialization of pkg/smooth and application to control vector
4123 mlosch 1.837 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
4124 gforget 1.836 o dependencies: pkg/profiles requires pkg/cal
4125 gforget 1.835 o pkg/profiles:
4126     - added option ALLOW_PROFILES_GENERICGRID
4127     -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
4128     that interpolation information (grid points and coefficients) is provided
4129     within the netcdf input files.
4130     -> sample matlab scripts can be found in MITgcm_contrib/gael
4131     that allow you to prepare netcdf input files.
4132     - also modified: cleaner include statements, cleaner error print statements,
4133     cleaner stops when error, and more tests of the netcdf input files consistency.
4134 jmc 1.834 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
4135 mlosch 1.830 o pkg/seaice:
4136 mlosch 1.833 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
4137     requires a new routine: seaice_diagnostics_fill.F
4138 mlosch 1.832 - make sure that seaice does not move if not forced (pressure replacement
4139     method, Hibler and Ip, 1995), changes results
4140 mlosch 1.830 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
4141     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
4142     It is turned off by default (=-1.), because it changes the results.
4143 mlosch 1.831 - make it possible to read AREA from a file, too.
4144 mlosch 1.830
4145 jmc 1.1203 checkpoint59c (2007/06/04)
4146 jmc 1.828 o add S/R and diagnostics for oceanic mixed-layer depth
4147     o move GMRedi call after all vertical mixing schemes (including KPP)
4148     o pkg/thsice:
4149     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
4150     (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
4151 mlosch 1.824 o pkg/obcs:
4152     - bug fix for balance code
4153 mlosch 1.822 o pkg/seaice:
4154 mlosch 1.825 - allow values of SEAICE_elasticParm > 1
4155 mlosch 1.826 - add new parameter SEAICE_evpTauRelax as an alternative
4156     to SEAICE_elasticParm
4157 mlosch 1.825 - make lsr boundary conditions free slip (by default), changes result
4158 mlosch 1.823 - add code for no slip boundary conditions for lsr
4159 mlosch 1.822 - set minimum of zeta to zero (and not 4e8) (changes results)
4160 mlosch 1.826 - add a cap on AREA after advecting AREA if seaice_growth is not called
4161 jmc 1.821 o change calculation of Visbeck K:
4162     - no longer depend on tapering scheme; instead, compute slope (limited
4163     by GM_maxSlope). this is equivalent to what was comuted before with
4164     clipping or linear tappering.
4165 jmc 1.828 - fix vertical averaging (wrong by 1/2 level)
4166 jmc 1.821 - leave the old version (but will not be maintained) within
4167     #ifdef OLD_VISBECK_CALC / #endif
4168 jmc 1.828 - update output of exp. ideal_2D_oce
4169 mlosch 1.820 o change error catch in calc_r_star to improve vectorization
4170 jmc 1.819 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
4171     add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
4172 heimbach 1.827 o adjoint:
4173     Re-organized adjoint checkpointing according to Matt Mazloff
4174     (but with modifs/completions/cleanups)
4175     Storing is now bundled into large arrays to optimized I/O
4176     (and second step in cleanup of the_main_loop)
4177 jmc 1.819
4178 jmc 1.1203 checkpoint59b (2007/05/16)
4179 jmc 1.818 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
4180     - export/import (between ocean & coupler) fields needed for ocean DIC.
4181 mlosch 1.817 o pkg/seaice:
4182     - get rid of three more exchanges seaice_calc_viscosities (required
4183     different loop boundaries in seaice_lsr and seaice_ocean_stress)
4184     - bug fix in seaice_ocean_stress (update of lab_sea required)
4185     - reduce loop boundaries to necessary minimum also in seaice_evp
4186     - go back to the old way of computing deltaC/Z as the adjoint likes that
4187     better
4188 dfer 1.816 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
4189     passive tracer to an Age Tracer) + update output.txt
4190 jmc 1.814 o pkg/exf:
4191 jmc 1.815 - implement A-grid / C-grid selection for wind-stress input files.
4192     - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
4193     for now, in exf_bulk_largeyeager04.F only :
4194     - change implementation for case where windspeed + 2. components wind-stress
4195     are read-in. AND use rhoConstFresh to convert evap.
4196     o pkg/seaice:
4197     - use correct EXCH_UV for wind-forcing (on A-grid).
4198     - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
4199     SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
4200     o pkg/exf:
4201 jmc 1.814 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
4202     EXF_INTERPOLATION:
4203     - merge global_with_exf/code version of exf_interp_read.F
4204     to the main code ;
4205     - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
4206     reading the file ; Important: This options needs to be defined to recover
4207     previous code.
4208     otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
4209     - no longer loose real*8 precision along the way when using exf_iprec=64.
4210 mlosch 1.811 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
4211 mlosch 1.813 - change discretisation of evp-solver in order to avoid another exchange
4212     (changes lab_sea) and clean up a little
4213     - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
4214     help the adjoint (this also changes the results slightly)
4215     - add a few "_d 0" where they had been missing in seaice_evp.F
4216     - cleaning up: remove unused seaice_calc_rhs.F
4217 jmc 1.810 o pkg/exf: some cleaning-up:
4218     - change various "constants" into runtime parameters
4219     - cleaned-up Large&Yeager04 routine which should eventually
4220     replace exf_bulkformulae.F (changed names of S/R and CPP)
4221     and merged various ALLOW_ATM_WIND options
4222     only used with thsice pkg (in thsice_get_exf.F):
4223     - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
4224     which are used when useStabilityFct_overIce=TRUE (= the default)
4225     - change default values of ice & snow emissivity and scale downward LW
4226     by ice & snow emissivity.
4227     o pkg/thsice:
4228 jmc 1.809 fix few little problems, in thsice_calc_thickn.F:
4229     - growth vertically (and not laterally) if iceFrac == iceMaskMax
4230 jmc 1.828 - melt only laterally if hIce < hThinIce (as the comments say)
4231 jmc 1.809 and in thsice_extend.F:
4232     - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
4233     - start to form ice as soon as the minimum ice-volume is reachable.
4234     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
4235     and cpl_aim+ocn
4236 mlosch 1.807 o pkg/kpp
4237 jmc 1.809 - move computation of surface related input fields to KPP into a new
4238     subroutine kpp_forcing_surf.F
4239 jmc 1.808 - remove wrong (within bi,bj loops) EXCH calls.
4240     - little cleaning (add argument myThid in last position, cvs header ...)
4241 jmc 1.809 - for now, fix conservation problem by exchanging KPPviscAz (may not
4242     be the best fix)
4243 mlosch 1.806 o pkg/seaice
4244     - check for inconsistent evp parameter/cpp-flag combination
4245     - remove leftover errIO flat for obsolete name list error handling
4246 heimbach 1.812 o OpenAD
4247     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
4248 mlosch 1.806
4249 jmc 1.1203 checkpoint59a (2007/05/01)
4250 mlosch 1.803 o pkg/seaice: some parameter clarifications and a little bit of clean up
4251 jmc 1.802 o pkg/thsice: rename run-time parameters:
4252     himin -> hIceMin
4253     himin0 -> hThinIce
4254     hihig -> hThickIce
4255     i0 -> i0swFrac
4256     transCoef -> bMeltCoef
4257     frac_energy -> fracMelting
4258     add new parameters: hNewIceMax, fracFreezing, dhSnowLin
4259     with default values (for now) that do not change the results.
4260     remove old version of thsice vars advection in pkg/seaice.
4261 jmc 1.801 o in FFIELDS.h:
4262     - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
4263     - make pLoad & sIceLoad always available (but still only used if
4264     ATMOSPHERIC_LOADING is #define).
4265 dimitri 1.799 o pkg/kpp: replaced _KPP_RL with _RL
4266 dimitri 1.798 o bug fixes for vertical diffusivity computations when both KPP and
4267 dimitri 1.883 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
4268     are no longer updating the vertical diffusivity array
4269     (passed as argument) but are (re-) setting those arrays.
4270 mlosch 1.795 o pkg/seaice: fix bug in evp solver, while doing that
4271     - change (improve?) discretization of stress computations for both
4272     cgrid-lsr and evp solver
4273     - add a new routine to compute strain rates
4274 mlosch 1.796 - the above changes lab_sea results
4275     - add no slip conditions for evp solver (off by default), lsr-version
4276     may follow
4277     - fix exchange for shear at Z-points (does not change lab_sea)
4278     - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
4279     (to force the user to pick a time step since there is not "safe" way
4280     of choosing it)
4281 mlosch 1.797 - add principal stress diagnostics
4282 mlosch 1.800 - rearrange fields for evp a little to avoid having to call a: too many
4283     exchanges and b: exchanges for stress trensor components which we do
4284     not have.
4285     - modify Hibler+Bryan (1987) stress coupling so that it reuses information
4286     of evp, complete rewrite for lsr case (latter is does not yet work
4287     in all cases)
4288 mlosch 1.794 o pkg/kpp: add code to have mixing in shelf ice caverns
4289 mlosch 1.804 - add myThid to all kpp routines (long overdue)
4290 mlosch 1.794
4291 jmc 1.1203 checkpoint59 (2007/04/19)
4292 heimbach 1.792 o pkg/exf:
4293     - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
4294     ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
4295     - move exf header files from lower_case.h to UPPER_CASE.h ;
4296     add missing cvs Header & Name
4297     - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
4298 heimbach 1.793 - add namelist param. selectStressGridPosition, exf_monFreq
4299     - retire many _CLIM routines, and remove data.exf_clim
4300     + params moved to data.exf
4301     + climsst, climsss now handled by exf_set_gen, i.e.
4302     climss?period=0 refers to constant field,
4303     climss?period=-12 to monthly forcing
4304     - split up namelists in data.exf
4305 mlosch 1.788 o pkg/seaice:
4306     - remove seaice_exch and seaice_exch_uv
4307     - remove superfluous exchange of theta
4308     - add myThid to seaice_budget_ocean/ice
4309 mlosch 1.790 - add new interface for atmospheric wind forcing (C-grid only)
4310     + new routine
4311     + two new field (taux, tauy for stress over ice)
4312     + removed one global field (DAIRN) for C-grid case only
4313 heimbach 1.792 o pkg/thsise
4314     - 2nd set of modifs for thsice adjoint in conjunction with exf
4315 heimbach 1.793 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
4316 mlosch 1.788
4317 jmc 1.1203 checkpoint58y_post (2007/04/15)
4318 dimitri 1.785 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
4319 dimitri 1.786 vertical diffusivity, similar to that in MOM4; turned on using
4320     #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
4321     diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
4322 dimitri 1.782 o Added capability for 3D specification of background vertical diffusion
4323     coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
4324     in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
4325     "data" file that contains the 3D vertical diffusivity coefficients.
4326 jmc 1.784 o ice dynamics (pkg/seaice) with thsice thermodynamics:
4327     - add code within pkg thsice to advect & diffuse sea-ice fields
4328     similar to (and will replace) what has been added in seaice_advdiff.F,
4329     but: - conserving Mass, Heat & Salt.
4330     - better when using non-linear advection scheme (not yet fully tested)
4331     - can also be used in atmospheric set-up (for now, only the diffusion).
4332 dimitri 1.783
4333 jmc 1.1203 checkpoint58x_post (2007/04/04)
4334 jmc 1.779 o IO option for global-file compact format:
4335     - add options when generating topology (utils/exch2/matlab-topology-generator)
4336     - add I/O capability (pkg/mdsio).
4337     - adapt utils/matlab/rdmds.m to read this format.
4338     for now long-line format not yet supported by pkg/mdsio (& exch2).
4339 mlosch 1.778 o shelfice: add a few diagnostics
4340    
4341 jmc 1.1203 checkpoint58w_post (2007/03/13)
4342 jmc 1.776 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
4343     rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
4344     (and replace horiVertRatio in NH code).
4345     Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
4346     and tutorial_plume_on_slope (sensitive to truncation)
4347 mlosch 1.774 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
4348     directly to drive seaice model (C-grid only)
4349     o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
4350     - reintroduce computation of wind from stress,
4351     - compute tau (in exf_bulkformulae.F) from windstress averaged to
4352     mass points to avoid tau = 0
4353 mlosch 1.775 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
4354 mlosch 1.774 o rdmnc.m: make it work with "global" files created with gluemnc
4355 jmc 1.773 o rdmnc.m : some improvements in dealing with singleton dimension
4356     (tested on all testreport mnc output files).
4357     o genmake2: disable pkg/profiles if netcdf test fails.
4358 jmc 1.772 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
4359 mlosch 1.771 o move call to cal_readparms up to make calendar parameters/variable available
4360     to all packages
4361    
4362 jmc 1.1203 checkpoint58v_post (2007/02/08)
4363 jmc 1.770 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
4364     useDynP_inEos_Zc tested.
4365 dimitri 1.769 o pkg/exf: changes to properly interpolate/mask/scale initial fields
4366 dimitri 1.768 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
4367     and portions thereof. See read_cs.txt for description and examples.
4368 jmc 1.767 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
4369     add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
4370     following the great-circle arc between those 2 points.
4371     o trap un-initialized variable with pathscale compiler on weddell.mit.edu
4372     (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
4373 jmc 1.766 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
4374     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
4375     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
4376     - still needs work (not working with some options ; efficiency to improve)
4377     and serious testing.
4378     - use this scheme for temperature & salinity in 2 advection test exp.:
4379     advect_xy & advect_xz, respectively.
4380    
4381 jmc 1.1203 checkpoint58u_post (2007/01/12)
4382 jmc 1.765 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
4383 jmc 1.764 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
4384     o testreport: add option "-skipdir" to skip some test.
4385     o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
4386     momentum calculation.
4387     o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
4388     o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
4389     remove checkpoint.F and the_correction_step.F (no longer used);
4390     do the k loop inside CYCLE_TRACER (supposed to be more efficient).
4391     o add option (linFSConserveTr) to correct for tracer source/sink due to
4392     Linear Free surface
4393 mlosch 1.763 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
4394     o pkg/thsice: fix reading mnc-pickups
4395    
4396 jmc 1.1203 checkpoint58t_post (2006/12/30)
4397 jmc 1.761 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
4398     o pkg/mdsio:
4399     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
4400     move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
4401     mdsio_write_field.F (S/R MDS_WRITE_FIELD);
4402     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
4403     - collect old S/R in one file: mdsio_rw_field.F (now just a call to
4404     either MDS_READ_FIELD or MDS_WRITE_FIELD )
4405     - new S/R (to replace MDSWRITEMETA), which allows to write more
4406     informations (variable names, time ...) to meta files.
4407     - modify rdmds.m to give back the meta file content.
4408 jmc 1.760 o pkg/diagnostics: change vertical interpolation to be safer, and more
4409     flexible (define p-levels to interpolate to in data.diagnostics);
4410     add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
4411     diagnostic pointer.
4412 mlosch 1.759 o pkg/seaice: more cleaning up of seaice_growth, added many comments
4413 mlosch 1.763 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
4414 mlosch 1.757 o fix multi-category seaice:
4415     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
4416     SEAICE_MULTICATEGORY
4417     - fix short wave heat flux
4418 jmc 1.758 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
4419     and allow to use EVP solver. Change forward lab_sea: test both EVP
4420     solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
4421 heimbach 1.756 o Initial check-in of lab_sea adjoint
4422     (very similar to natl_box_adjoint/code_seaice)
4423     * used C-grid and EVP solver
4424     * used KPP, GM/Redi
4425     * uses inAdExact=.TRUE.
4426     * gradient checks fail for both ADM and TLM
4427     due to sensitive snow melt code in seaice_grwoth (look for "JZ")
4428     f.d. gradients actually seem more problematic than ADM, TLM gradients;
4429     issue is related to forward mismatch between g77 an ifort
4430 mlosch 1.755 o pkg/seaice: overhaul of thermodynamics
4431     - growth.F and groatb.F are replaced by new routine seaice_growth.F
4432     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
4433     - move a few global fields out of SEAICE.h into seaice_growth.F and
4434     make them 2D (FICE/QNETO/ ...)
4435     - remove FO (it is the same as QNETO)
4436     - introduce a few local fields to avoid modifying external fields such
4437     as atemp, etc.
4438    
4439 jmc 1.1203 checkpoint58s_post (2006/12/11)
4440 dimitri 1.753 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
4441     changed exf_set_gen.F so that
4442     genperiod=0 means input file is one time-constant field and
4443     genperiod=-12 means input file contains 12 monthly means
4444 jmc 1.752 o CG2D: use pre-computed solver main-diagonal (stored in common block);
4445     this affects truncation error ; generate new output file for exp. which
4446     fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
4447     global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
4448     ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
4449     MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
4450     tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
4451     vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
4452 jmc 1.751 o start implementation of deep-atmosphere and anelastic formulation
4453 jmc 1.750 o verification: remove 2nd copy of input files and use script "prepare_run"
4454     to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
4455 mlosch 1.749 o mom_common/vecinv/fluxform: fix a few initialisation isssues
4456 gforget 1.748 o profiles: fix for multithreaded case
4457    
4458 jmc 1.746 o diagnostics: rename few diags:
4459     s/'PRESSURE'/'RCENTER '/g
4460     s/'TICE '/'oceFreez'/g
4461     s/'TAUX '/'oceTAUX '/g
4462     s/'TAUY '/'oceTAUY '/g
4463     s/'SWFLUX '/'oceQsw '/g
4464     s/DIFx/DFxE/g
4465     s/DIFy/DFyE/g
4466     and add few ocean-forcing diagnostics:
4467     atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
4468 dimitri 1.747 o modifications to pkg/seaice/growth.F and budget.F, which change results of
4469     lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
4470     as actual snow thickness. It now refers everywhere to effective snow
4471     thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
4472 jmc 1.746
4473 jmc 1.1203 checkpoint58r_post (2006/11/17)
4474 dimitri 1.744 o modifications to pkg/seaice/growth.F, which change results of
4475     lab_sea experiment: fixes pertain to melting snow over open water, to
4476     masking EVAP under sea ice, and to using the correct AREA variable for
4477     computations of EVAP, PRECIP, HSNOW, and GHEFF
4478 edhill 1.743 o add ability to read bathy, salt, and theta using MNC (off by def)
4479 mlosch 1.742 o add flooding algorithm and advection of HSNOW for pkg/seaice;
4480     both are turned off by default and do no change any results
4481 jmc 1.741 o seaice advection with pkg/thsice: a step toward the use of non-linear
4482     advection scheme, but #ifdef or commented out for now (requires more EXCH).
4483 jmc 1.739 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
4484     (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
4485     in natl_box (affects results @ truncation level: update output.txt)
4486     o multi-threading and IO:
4487 jmc 1.738 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
4488     - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
4489     (needed to work with SingleCpuIO): tested in all verif. exp.
4490 jmc 1.737 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
4491     affects the results (but none of the verification test uses this scheme).
4492 heimbach 1.736 o Adding some pkg/diagnostics capability to pkg/seaice
4493     (will certainly be subject to changes)
4494 heimbach 1.740 o ctrl: adding new control variables:
4495     lwflux, lwdown, evap, snowprecip, apressure, runoff
4496 heimbach 1.736
4497 jmc 1.1203 checkpoint58q_post (2006/10/20)
4498 dimitri 1.734 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
4499     1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
4500     high_res_cube configuration by 4% on Columbia.
4501 jmc 1.733 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
4502     add (in global_with_exf/code) a version of EXF_INTERP_READ without
4503     dynamical allocation (seems to work in multi-threaded).
4504     o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
4505     single CPU io) so that TAF does not have to see EESUPPORT.h
4506 jmc 1.727 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
4507    
4508 jmc 1.1203 checkpoint58p_post (2006/09/08)
4509 mlosch 1.726 o obcs: stop if obcs is used with useCDscheme = .true.
4510 mlosch 1.723 o shelfice:
4511     - fix a sign error so that no slip at shelfice interface works
4512     - remove stop for combination non-hydrostatic code and shelfice. That does
4513     not mean, that the results are correct, but at least they are numerically
4514     stable
4515 dfer 1.721 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
4516 heimbach 1.724 o added adjoint exch routined for all exch*3d* routines
4517     and updated flow directives
4518 dfer 1.721
4519 jmc 1.1203 checkpoint58o_post (2006/08/28)
4520 jmc 1.720 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
4521     remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
4522 jmc 1.719 o change controling S/R for writing pickup file (new S/R do_write_pickup)
4523     and clean-up reading/writing of pickup files.
4524     o fix local version of read/write pickup (NH part) in rotating_tank/code
4525 jmc 1.718 o simplify EXCH interface:
4526     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
4527     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
4528 edhill 1.717 o added the regrid package
4529 mlosch 1.716 o shelfice:
4530     - add a simple boundary layer scheme to reduce noise
4531     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
4532 jmc 1.718
4533 jmc 1.1203 checkpoint58n_post (2006/08/14)
4534 jmc 1.713 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
4535     local variable (not in common block).
4536 jmc 1.712 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
4537     - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
4538     - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
4539     to work with SingleCpuIO.
4540 jmc 1.711 o add "_d 0" to real constant of pkg/cfc subroutines ;
4541     update exp. cfc_exemple & tutorial_cfc_offline output files.
4542 jmc 1.710 o multi-threading and IO:
4543     - all threads call READ_FLD S/R (needed if using SingleCpuIO):
4544     (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
4545     - barrier before and after reading.
4546     - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
4547     - avoid using MDS_WRITELOCAL for LAND pkg output.
4548     - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
4549     common-block variables ; Allows multi-threading with master-thread IO.
4550 jmc 1.709 o change default MAX_NO_THREADS from 32 to 4 ;
4551     and stop cleanly when MAX_NO_THREADS is too small.
4552     o add S/R BAR_CHECK to check multi-threaded barrier synchronization
4553    
4554 jmc 1.1203 checkpoint58m_post (2006/07/17)
4555 jmc 1.707 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
4556     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
4557 jmc 1.706 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
4558     keep global_ocean.90x40x15 (for AD testing) with former secondary test
4559     (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
4560     o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
4561     add MITgcm_tutorials (= code + all the tutorials)
4562 gforget 1.705 o ecco, option to compute cost for total ssh (mean+anom)
4563 gforget 1.704 o consistent with addition of ptracer and ssh in pkg/profiles
4564 gforget 1.703 o profiles: adding ptracer and ssh
4565 jmc 1.702 o testreport: change multi-test output-file name
4566     (from output.txt.{name} to output.{name}.txt)
4567 jmc 1.712 o profiles: now ok for mutli-tiles case
4568 mlosch 1.700 o seaice: add 4 parameters for different advection schemes for area,
4569     (effective) seaice thickness, enthalphy, and snow height. Their default
4570     is the standard parameter SEAICEadvScheme
4571 jmc 1.699 o calc_gw:
4572     - add cosFacU in zonal viscous flux (harmonic.visc.).
4573     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
4574     of tutorial_plume_on_slope.
4575     o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
4576 jmc 1.698 o calc_gw: true flux-form, account for horizontal grid spacing.
4577     update rotating_tank results, but not plume_on_slope (affected at
4578     truncation level, 11 digits).
4579    
4580 jmc 1.1203 checkpoint58l_post (2006/07/12)
4581 jmc 1.698 o calc_gw:
4582     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
4583     - remove side-drag for now (need to fix it); update plume_on_slope results.
4584     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
4585 heimbach 1.695 o commit code to make SST/SSS weights spatially variable
4586     (based on either variable in-situ or variable initial T/S weights)
4587 heimbach 1.696 o pkg/ecco:
4588     * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
4589     now based on horizontally varying weights wthetaLev, wsaltLev
4590     * cost_averagesflags now returns year indices in addition to day, month
4591     * sflux balance is performed on annual basis
4592     (sflxumm, sfluxmm2, bal_sfluxmm)
4593     * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
4594     including separate counting and multipliers
4595 heimbach 1.697 o pkg/rbcs
4596     * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
4597 jmc 1.694
4598 jmc 1.1203 checkpoint58k_post (2006/07/06)
4599 jmc 1.692 o testreport:
4600     - always build in dir. "build" (if not there, mkdir build instead of building
4601     & running in input)
4602     - run in dir run (if it exists), in build otherwise.
4603     - call prepare_run (if input/prepare_run exists)
4604     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
4605 dimitri 1.691 o pkg/exf modifications to interpolation and rotation routines for more
4606     reasonable treatment of North Pole singularity: for tracers North Pole
4607     value is set to northernmost zonal-mean value, for zonal velocity it is
4608     set to zero, and for meridional velocity it is set to northernmost value.
4609 mlosch 1.690 o pkg/exf/exf_check_range.F
4610     - add tile index to diagnostics and move stop statement to the very
4611     end of the routine.
4612 jmc 1.689 o pkg/diagnostics: (diagnostics_main_init.F)
4613     define title of isomorphic variables according to the current config.
4614 jmc 1.687 o pkg/thsice with pkg/seaice dynamics:
4615 jmc 1.688 - fix domain of computation (interior only, required for exf) and do exchanges
4616     - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
4617 jmc 1.686 o towards a standard way of dealing with multi-threading in MONITOR
4618     and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
4619 baylor 1.685 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
4620     to W momentum equation in nonhydrostatic and quasihydrostatic runs.
4621 jmc 1.684 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
4622 jmc 1.683 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
4623     o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
4624     (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
4625 jmc 1.682 o tracer advection:
4626     - clean-up and simplify calc_common_factors.F
4627     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
4628     advection subroutine (but still not used within DST advection S/R)
4629 jmc 1.681 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
4630    
4631 jmc 1.1203 checkpoint58j_post (2006/06/15)
4632 heimbach 1.680 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
4633     from file (collects calls previously in FORWARD_STEP)
4634     o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
4635 heimbach 1.679 o adjoint store dir. adjusted accordingly
4636 heimbach 1.680 o genmake2
4637     replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
4638 heimbach 1.679
4639 jmc 1.1203 checkpoint58i_post (2006/06/14)
4640 mlosch 1.677 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
4641     on wind stress (SEAICEstressFactor defaults to 1.)
4642 jmc 1.676 o Total number of Timers is finite (<=40): comment out 2 non-essential one
4643     in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
4644 jmc 1.675 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
4645     on CS-grid: no longer loosing mass.
4646 jmc 1.674 o exf & curvilinear-grid: no longer modify longitude xC & xG.
4647 mlosch 1.670 o pkg/ggl90: fix sloppy output and fix a bug
4648 dimitri 1.672 o pkg/seaice: added SEAICEuseEVPpickup parameter
4649     - Set to false in order to start EVP solver with
4650     non-EVP pickup files when using SEAICEuseEVP
4651 mlosch 1.673 - fix sign error in diffusion in seaice_calc_rhs
4652 mlosch 1.670
4653 jmc 1.1203 checkpoint58h_post (2006/06/07)
4654 heimbach 1.669 * Modifications for bottom topography control
4655     o replace hFacC by _hFacC at various places
4656     o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
4657     o add non-self-adjoint cg2d_nsa
4658     o update autodiff support routines
4659     o re-initialise hfac after ctrl_depth_ini
4660     o works for 5x5 box, doesnt work for global_ocean.90x40x15
4661     * Adding verification for 5x5 box (4-layer) bottom topography control
4662    
4663 jmc 1.1203 checkpoint58g_post (2006/06/07)
4664 jmc 1.671 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
4665     used for mean seasonal cycle, mean diurnal cycle); add an example
4666     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
4667 mlosch 1.667 o pkg/ggl90:
4668     - add parameter (minimum surface kinetic energy)
4669     - fix bug (avoiding division by zero)
4670 mlosch 1.665 o couple pkg/thsice to pkg/seaice:
4671     - modify advection in seaice to accomodate new scalar fields to be advected
4672     - only muliDimAdection scheme work with seaice/thsice
4673     - mapping of thsice-variables to seaice-variables, back and forth
4674     - does not break the verification experiments, but does not give the
4675     desired results either
4676     o pkg/seaice
4677     - make (default) second order advection a bit less confusing?
4678    
4679 jmc 1.1203 checkpoint58f_post (2006/06/05)
4680 mlosch 1.662 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
4681     to pkg/seaice):
4682     - new routines thsice_map_exf and thsice_get_exf provide the interface
4683     - add an additional formal parameter to thsice_solve4temp
4684 heimbach 1.661 o pkg/exf:
4685     - add new fields wspeed, snowprecip (to be able to couple to thsice)
4686     - correct Stefan-Boltzmann constant
4687     - new parameter for longwave surface emittance
4688     - separate some stuff from exf_bulkformulae into new routines
4689     exf_radiation, exf_wind
4690 mlosch 1.662 - add new parameters and constants: longwave emissivity for ocean, ice
4691     and snow, evaporation parameters over ice
4692 mlosch 1.663 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
4693     either wind from stress or stress from wind
4694 jmc 1.660 o pkg/thSIce:
4695     - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
4696     - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
4697     and THSICE_CALC_THICKN
4698     - for now, call to THSICE_GET_BULKF remains inside i,j loops.
4699     - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
4700     to make debugging easier.
4701     - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
4702     o pkg/bulk_force:
4703     - clean-up comments and parameters ;
4704     - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
4705 jmc 1.659 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
4706     generate new output for test-experiment: aim.5l_cs.thSI
4707 jmc 1.658 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
4708 heimbach 1.661 testreport accordingly
4709 jmc 1.658
4710 jmc 1.1203 checkpoint58e_post (2006/05/17)
4711 heimbach 1.656 o SEAICE_CGRID adjoint done
4712 heimbach 1.654 o R_STAR adjoint implemented.
4713     * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
4714     * need to sort out init. of h0facc, etc.
4715 heimbach 1.655 o Make pkg/profile fully independent of ecco,cost, etc. stuff
4716     to be able to use it in pure forward.
4717 heimbach 1.653
4718 jmc 1.1203 checkpoint58d_post (2006/04/21)
4719 jmc 1.651 o upgrade simple test-experiment to tutorial example:
4720     step.1: duplicate the experiment and (step.2) will remove the old copy.
4721     tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
4722     tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
4723     tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
4724     tutorial_global_oce_biogeo <- copy of dic_example
4725     tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
4726     tutorial_plume_on_slope <- copy of plume_on_slope
4727     tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
4728     tutorial_global_oce_optim <- empty for now (David ?)
4729     tutorial_global_oce_in_p <- copy of global_ocean_pressure
4730     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
4731 gforget 1.650 o correct a sign problem in cost_scat.F
4732 mlosch 1.649 o obcs and ptracers: fix boundary conditions for advections schemes
4733     with larger stencil
4734 heimbach 1.648 o thsice adjoint: start
4735 mlosch 1.647 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
4736     completeness
4737 mlosch 1.646 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
4738     and COSINEMETH_III, add comments in default CPP_OPTIONS.h
4739 heimbach 1.645 o ptracers adjoint:
4740     * avoid extensive recomputatations
4741     * fix missing re-init. of gptr (missed by TAF)
4742 mlosch 1.644 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
4743     me to turn off the excessive output to STDOUT that this package produces
4744 jmc 1.643 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
4745     and add those terms in Vector-Invariant formulation.
4746 gforget 1.642 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
4747     if the control period (xx_hfluxperiod etc) is 0
4748     o in profiles pkg, clean routines and fix details
4749     o in ecco pkg, reading ssh data:
4750     fix problem in case the model does not start at iter0=0
4751 mlosch 1.640 o fix mnc-pickup/restart for ptracers
4752 heimbach 1.641 o new package prifiles:
4753     code to compute profile-based cost by Gael Forget
4754 heimbach 1.639 (modifs in ecco, ctrl, autodiff)
4755 heimbach 1.641 o Benign bug fix in initialization (spotted by M. Mazloff) of
4756     ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
4757 heimbach 1.639
4758 jmc 1.1203 checkpoint58c_post (2006/03/23)
4759 heimbach 1.638 o adjoint: finish NLFS adjoint and provide reference output in
4760     verification/global_ocean.90x40x15/results_ad_nlfs
4761 mlosch 1.637 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
4762     documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
4763     SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
4764     with SEAICE_CGRID defined.
4765 jmc 1.636 o move calendarDumps from "data" to "data.cal" and clean-up the code
4766     with a simple call to pkg/cal S/R: CAL_TIME2WRITE
4767     o add useEXF & useCAL flags (for now, set in hard-coded way)
4768 jmc 1.635 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
4769     (were missing in NH mode, and wrong in quasihydrostatic mode).
4770     waiting for Chris updated version of calc_gw to add those CALLs.
4771     o fix bug in quasihydrostatic S/R ;
4772     add a test for this option: global_ocean.90x40x15.qshyd
4773 jmc 1.634 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
4774     (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
4775     o add on/off flag useOffLine for package OFFLINE
4776 mlosch 1.630 o seaice:
4777     - modify advection so that it works also on the C-grid
4778     - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
4779     problem in multi-tile runs with C-grid
4780 mlosch 1.633 - add flags for clipping ice velocities and/or masking solver forcing
4781 mlosch 1.631 - fix drag (ocean on ice) formulation and a bug that caused noise in the
4782     C-grid solver
4783 mlosch 1.632 - added a few comments to seaice_diffusion.F
4784     - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
4785     are now exclusive)
4786     - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
4787     required re-ordering the code a little:
4788     + make DAIRN global variable (defined in SEAICE)
4789     + move computation of the viscosities eta and zeta into a new separate
4790     routine (because I need to recompute them in seaice_ocean_stress.F)
4791 mlosch 1.629
4792 jmc 1.1203 checkpoint58b_post (2006/03/13)
4793 jmc 1.627 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
4794     update output.txt of exp. aim.5l_cs.thSI
4795 edhill 1.626 o various mnc cleanups and improvements:
4796     + shrink lookup tables by factor of ~4
4797     + better error reporting when running out of lookup space
4798     + able to handle longer path/file names (up to 500 chars)
4799 heimbach 1.625 o adjoint:
4800     - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
4801     - TBD: "hidden" mom_vecinv recomp. in dynamics
4802 jmc 1.624 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
4803     (allow to differentiate between forcing components using new integer flags:
4804     momForcingOutAB=1/0 & tracForcingOutAB=1/0)
4805     and add new flag to put Dissipation tendency out of Adams-Bashforth.
4806 heimbach 1.623 o ecco
4807     - enable trend removal from SSH anomaly obs.
4808     o adjoint
4809     - a fix for PmEpR when #undef EXACT_CONSERV
4810     - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
4811     - try to fix "hidden" recomp. in forward_step for NLFS
4812     (NLFS seems broken sometimes after I checked it in)
4813 mlosch 1.622 o seaice:
4814     - add c-grid version of the dynamic solver:
4815     + three new routines that are the c-grid substitute lsr, dynsolver
4816     and ostres
4817     + put a few fields that were local to dynsolver into global common
4818     blocks, so that I can move the computation of stresses etc into
4819     seaice_lsr (saves coding but may break the adjoint).
4820     - replace more hardwired parameters by runtime parameters
4821     - add ice masks that mask the rhs of the implicit solvers where there
4822     is no ice (commented out in seaice_dynsolver, because i am not sure
4823     if this works properly), eventually this should replace the clipping
4824     of ice velocities in seaice_dynsolver to +/-40cm/s.
4825 edhill 1.621 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
4826     include it only where its needed
4827 mlosch 1.620 o move balancing of fluxes before the call of external_forcing_surf
4828 mlosch 1.619 o seaice:
4829     - correct units of turning angles (now they are really in degrees)
4830     - move computation of GWATX/Y out of main routine into dynsolver
4831     - initialize GWATX/Y in seaice_init
4832 jmc 1.618 o Apply mask on Fresh-Water flux (needed for SSH forcing).
4833 mlosch 1.619 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
4834 mlosch 1.617 o seaice: add runtime flags for turning angles (default to zero)
4835 heimbach 1.616 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
4836     and trend from exf forcing and ctrl control adjustments
4837     o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
4838     (since checkpoint57x_post)
4839 jmc 1.615 o change the default rotation period to 86164.s = the Earth rotation
4840 jmc 1.614 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
4841     and based on a reference stratification. Tested within hs94.cs-32x32x5.
4842 mlosch 1.613 o seaice advection: add code for choosing between the default (2nd order
4843     central differences) and multiDim advection schemes provided by
4844     pkg/generic_advdiff
4845 mlosch 1.611 o seaice:
4846     - removed all references to SEAICE_GRID.h fields from
4847     dynsolver, advect, diffus, lsr, without changing the results of lab_sea
4848     (cubed-sphere configuration will change a little)
4849     - grid computations in seaice_init are obsolete now.
4850     - cleaned up code a little so that is easier to read (hopefully).
4851 mlosch 1.613 - added new (better?) discretizations of default advection and diffusion
4852     (turn on with SEAICEuseFluxForm)
4853     - replace 1 in 3d global fields by kSurface in growth.F
4854 mlosch 1.611
4855 jmc 1.1203 checkpoint58a_post (2006/02/13)
4856 mlosch 1.612 o seaice:
4857     - bug fix in advect.F
4858 mlosch 1.608 o shelfice:
4859     - separate shelfice load anomaly from pload (breaks with time
4860     dependent forcing), => introduce constant field shelficeLoadAnomaly.
4861     Its default is 0., but it may be computed more cleverly from (unknown)
4862     t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
4863     done offline. A good approximation of the pressure load anomaly is
4864     necessary to avoid large initial adjustment processes underneath
4865     deep-reaching shelfice.
4866 mlosch 1.609 - small fix in ISOMIP shelfice_thermodynamics
4867     - add more sophisticated thermodynamics of Hellmer (1989), this is
4868     now the default
4869     - give a few constants more intuitive names
4870 mlosch 1.607 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
4871     if bulk formulae are used in long integration (especially EmPmR). Turn
4872     on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
4873     if balancePrintMean, the imbalance that is substracted is printed to
4874     STDOUT.
4875 jmc 1.606 o fix bug (typo) in obcs_apply_eta.F
4876 mlosch 1.605 o add a new package shelfice which enables us to model the circulation
4877     underneath shelf-ice with draughts of hundreds of meters.
4878     - works
4879     - to do: + include improved thermodynamics
4880     + check whether kSurfC (from model/inc/SURFACE.h) can be used
4881     instead of new field kTopC
4882     + can we use topoFile, Ro_surf and existing code in ini_depth.F
4883     instead of new field R_shelfIce and new code in ini_depth.F
4884     and ini_mask_etc.F?
4885 mlosch 1.608 + adjust vertical mixing schemes?
4886 mlosch 1.604 o seaice pkg:
4887     - add a cpp-flag to include a simple formula for a salinity dependent
4888     freezing point of sea water at the surface
4889     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
4890     meridional stresses are now different (and hopefully correct)
4891 jmc 1.602 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
4892     update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
4893     and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
4894 jmc 1.601 o pkg/diagnostics: add options and parameters for regional-statistics
4895     diagnostics ; define regions by reading a region-mask from a file
4896     (might add other options later)
4897 jmc 1.600 o pkg/bulk_force:
4898     - add option and parameters to use AIM surface-flux formulae.
4899     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
4900     others forcing fields (defined in PARM05, parameter file "data") are loaded
4901     from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
4902     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
4903     - use the right EXCH call for uwind,vwind (to work on CS-grid).
4904     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
4905     and parameters (note: calcWindStress replaces .NOT.readwindstress).
4906     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
4907    
4908 jmc 1.1203 checkpoint58 (2006/01/12)
4909 edhill 1.598 o add "--embed-source" option to genmake2 which, when the supporting
4910     tools can be compiled (as determined by genmake2) will turn on the
4911     embed_files package which then embeds the entire MITgcm source code
4912     (*.[fFhc] + Makefile) used for the build within the executable
4913     - requested by CNH but off by default
4914     - adds a paltry <9MB to the mitgcmuv executable in most cases
4915     - only writes the output when useEMBEDSRC in eedata is true
4916 heimbach 1.597 o clean up 3-dim. relaxation codes:
4917     * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
4918     * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
4919     * Thanks to Tom Haine for testing!
4920    
4921 jmc 1.1203 checkpoint57z_post (2005/12/31)
4922 jmc 1.593 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
4923     affects output (@ truncation level) of exp. plume_on_slope ; updated.
4924 mlosch 1.592 o fix the pickup behavior for obcs in combination with ptracers
4925     o fix a bug in ptracers_external_fields_load
4926     o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
4927     affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
4928     o transfered surface NH pressure to eta field (if exactConserv).
4929 jmc 1.589 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
4930     and update lab_sea output.txt file.
4931 heimbach 1.590 o completing 3-dim. relaxation code: additional term
4932     1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
4933     in S/R EXTERNAL_FORCING_T (file external_forcing.F)
4934     * At compile time, in "EXF_OPTIONS.h" set
4935     #define ALLOW_CLIMTEMP_RELAXATION
4936     #define ALLOW_CLIMSALT_RELAXATION
4937     * At runtime in "data", under &PARM03 set (e.g., units in seconds)
4938     tauThetaClimRelax3Dim = 15552000.0,
4939     tauSaltClimRelax3Dim = 15552000.0,
4940     * 3 cases:
4941     1) Use a constant-in-time 3-dim. field
4942     2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
4943     3) Real-time relax. to time-evolving prescribed field
4944 heimbach 1.595 o Adding Laplacian-type smoothness constraint on
4945     initial and boundary (forcing) controls (ic, bc)
4946     * enable at compile-time via
4947     ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
4948     * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
4949 heimbach 1.594 * Absolute scale somewhat unclear so far
4950     * no area weighting was included since no other cost term does so far
4951 jmc 1.589
4952 jmc 1.1203 checkpoint57y_post (2005/12/08)
4953 heimbach 1.588 First step for a NLFS adjoint
4954     o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
4955     o new init. routines for calc_r_star, calc_surf_dr
4956     o still need to deal with ini_masks_etc
4957     o testreport seemed happy
4958 jmc 1.1203 checkpoint57y_pre (2005/12/08)
4959 heimbach 1.587
4960 jmc 1.586 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
4961 stephd 1.585 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
4962 stephd 1.584 o add new offset feature to offline pkg (plus minor cleanup)
4963     o cfc fixes for final year of integration
4964     o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
4965     be in GCHEM_OPTIONS).
4966    
4967 jmc 1.1203 checkpoint57x_post (2005/12/04)
4968 jmc 1.583 o fix testreport Pb in multiple test experiment.
4969 edhill 1.582 o cleanup our namelist syntax in verification:
4970     - make it more F95 standards compliant (some work still needed)
4971     - allows the vast majority of our tests to work with gfortran
4972 jmc 1.580 o Non-Hydrostatic:
4973     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
4974     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
4975 jmc 1.579 o Allow to apply AB on T,S rather than on AB(gT,gS):
4976     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
4977     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
4978     time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
4979     - need a "clever" read_pickup to restart from the other AB formulation
4980 jmc 1.578 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
4981     o remove some unused variables (reduces number of compiler warnings)
4982 heimbach 1.581 o adjoint
4983     * Disable useVariableViscosity for adjoint for time being
4984     (there are a number of extensive recomputations)
4985     * Initialize certain variables needed for adjoint
4986 jmc 1.578
4987 jmc 1.1203 checkpoint57w_post (2005/11/03)
4988 jmc 1.576 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
4989     fix the singleCpuIO RS version of MDSWRITEFIELD
4990     and add a WARNING if using globalFiles=T with multi-processors.
4991 jmc 1.575 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
4992     using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
4993 jmc 1.576 o tracer advection scheme:
4994 jmc 1.574 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
4995     those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
4996     was not very convenient).
4997     add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
4998     (further tests needed for the implicit DST & Flux-Limiter schemes).
4999 mlosch 1.573 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
5000     and sRef for convenience, handy, when you want to initialize
5001     ptracers in a large domain with a constant non-zero value. Also,
5002     untangle ptracers_init.F a little.
5003    
5004 jmc 1.1203 checkpoint57v_post (2005/10/13)
5005 jmc 1.572 o change dome exp. to use variable viscosity in side-drag terms.
5006 edhill 1.570 o remove all the files from the cfc_offline test since they are now
5007     incorporated into tutorial_cfc_offline which has been producing
5008     identical results for a few days of testing
5009 jmc 1.571 o add new parameter: sideDragFactor to enable half-slip-side BC
5010     and change side-drag S/R to use viscosity from mom_calc_visc
5011     (can switch back by setting sideDragFactor=0.); affects results at
5012     truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
5013     global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
5014 jmc 1.569 o vorticity & strain are now computed without masking, to account for
5015     no-slip-side BC in variable viscosity calculation ; mask is applied
5016     anyway later on, before computing advection/coriolis terms.
5017 mlosch 1.573 o modify exp4 to test new obcs support for reading from external files
5018 mlosch 1.568 and for passive tracers
5019 mlosch 1.567 o fix behavior of ptracers_monitor when monitor output is written to a
5020     netcdf-file; still not independent of monitor.F (writes in the same
5021     file).
5022 jmc 1.566 o change default value of tRef (put a uniform, meaningful value for ocean
5023     & atmos) and initialize sRef (was missing, as Martin mentioned).
5024 baylor 1.565 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
5025     to be proportional to enstrophy dissipation length. Thus,
5026     viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
5027     This is now consistent with Smagorinsky and with the manual.
5028    
5029 mlosch 1.564 checkpoint57u_post
5030 mlosch 1.562 o OBCS and PTRACERS: add open boundary support for passive tracers
5031     - either use homogenous (pseudo) v.Neumann conditions or prescribe
5032     OB-values from file; this is not different from the way theta and salinity
5033     are treated
5034     - however, Orlanski-radiation conditions are not supported, and the model
5035     will stop if you use pTracers and Orlanski at the same time.
5036     - beefed up the rountine obcs_external_fields_load: now only those open
5037     boundary values are overwritten with values from files for which there
5038     are really files, otherwise the OB-fields remain untouched. This makes
5039     it possible to use different OBs at different ends of the domain (as
5040     with EXF)
5041 jmc 1.561 o reduce number of exch calls in shap_filt (s2).
5042 jmc 1.560 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
5043     truncation level) 4/5 MLAdjust test results (11&12 digits match).
5044    
5045 jmc 1.1203 checkpoint57t_post (2005/10/03)
5046 jmc 1.558 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
5047     o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
5048     same truncation, independent of the face number: affects affects several
5049     test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
5050 jmc 1.557 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
5051 jmc 1.558 note that biharmonic viscosity + no-slip was not tested in any experiment.
5052 jmc 1.556 o fix bug in non-linear free-surf side-drag ; generate new output for
5053     global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
5054 edhill 1.555 o make mnc honor the writeBinaryPrec flag for most kinds of output
5055 edhill 1.554 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
5056 jmc 1.553 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
5057     error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
5058 jmc 1.552 o add brackets in multi-terms sum to get same truncation, independent of
5059     the face number (manage to get exactly same value of gU,gV at the cs-edge)
5060     affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
5061 baylor 1.551 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
5062     and viscA4Remax, which allow one to limit the minimum viscosity by specifying
5063     a maximum grid-scale Reynolds number. Also, changes all length calculations
5064     in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
5065     Suggested values of viscosity parameters found in mom_calc_visc.
5066     Many new viscosity diagnostics available.
5067 jmc 1.550
5068 jmc 1.1203 checkpoint57s_post (2005/09/20)
5069 baylor 1.549 o Add clearing-house for viscosity calculations, mom_calc_visc and
5070     correct numerous bugs in LeithD and Smagorinsky discretizations.
5071     mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
5072     used simultaneously, and to be used in mom_vecinv and mom_fluxform.
5073     Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
5074     and with Strain-Tension viscous term calculation (mom_hdissip.F).
5075     The Strain-Tension form is now called with useStrainTensonVisc=.true.
5076     ViscAhStrain and viscAhTension are now retired.
5077 jmc 1.550 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
5078 edhill 1.547 o In response to JMC's bug report, genmake2 now ignores any soft-links
5079     that it finds in the *current* directory when searching for files.
5080     Soft-links found in any other source directories will still work as
5081     they did before.
5082 edhill 1.546 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
5083     a C routine to unlimit the stack size
5084 edhill 1.545 o mnc-ify pkg/aim snapshot vars
5085 edhill 1.544 o mnc-ify pkg/land as requested by Daniel
5086 edhill 1.543 o various changes to mnc including:
5087     - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
5088     - output can now be grouped so that all files within a group
5089     change the ITER portion of their names in lock-step together
5090     - can now read ("global") PER-FACE (in addition to PER-TILE) files
5091     and works with both EXCH1 and EXCH2 (but needs more testing)
5092     - writing works for all verification test cases w/ g77 on Linux
5093    
5094 jmc 1.1203 checkpoint57r_post (2005/09/07)
5095 edhill 1.541 o make MNC variable initialization happen earlier
5096 jmc 1.540 o add diagnostics for (almost) each term of the momentum Eq.
5097 jmc 1.537 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
5098 jmc 1.536 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
5099     o remove MINIMAL_TAVE_OUTPUT option ;
5100     add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
5101 jmc 1.535 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
5102     allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
5103 heimbach 1.538 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
5104     o add time-dependent SST, SSS control
5105 heimbach 1.539 o cost terms in ecco/ modularized (new cost_generic.F)
5106     o cost_averages routines are modularized (new cost_averagesgeneric.F)
5107     o new infrastructure for seaice model vs. obs misfits in seaice/
5108     * driver from the_main_loop.F is seaice_cost_driver.F
5109     * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
5110     * gradient check in Exp. 6a of natl_box_adjoint/
5111     o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
5112     (see README file)
5113 jmc 1.535
5114 jmc 1.1203 checkpoint57q_post (2005/08/19)
5115 jmc 1.533 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
5116 edhill 1.531 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
5117     - bug was reported by Jean-Michel and Ian Fenty
5118 jmc 1.532 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
5119     update exp. cpl_aim+ocn output.
5120 heimbach 1.530 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
5121     Needed for high-res. runs with large global files
5122     to be able to limit tapelev size
5123     o Changed some tests for adjoint:
5124     * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
5125     * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
5126     * global_ocean.90x40x15/ back to default 3-level checkpointing
5127 heimbach 1.534 o Modifications to enable scripted COMMON to MODULE conversion
5128     * verification/OpenAD/code/ has necessary scripts and description;
5129     * converts, compiles and runs successfully;
5130 heimbach 1.530
5131 jmc 1.1203 checkpoint57p_post (2005/08/01)
5132 jmc 1.529 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
5133     o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
5134     (already the case for some pkgs, including recent MNC_init, e.g. thsice)
5135     o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
5136 jmc 1.527 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
5137     (was already the case for dissipation with mom_vecinv,
5138     and also the case for grad.PhiHyd when staggered-timeStep)
5139     This will allow to put dissipation out-off the AB time-stepping.
5140     Unfortunately, affects truncation error. Update output of exp. that "fails"
5141     (cg2d matching number) and leave the others for later: front_relax(10),
5142     global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
5143     matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
5144    
5145 jmc 1.1203 checkpoint57o_post (2005/07/30)
5146 edhill 1.525 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
5147     (2) its ready to be documented during the 20050801 DocFest
5148 edhill 1.524 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
5149     for ideal_2D_oce and lab_sea on linux_ia32_g77
5150 heimbach 1.526 o set to #undef CTRL_SET_OLD_MAXCVARS_30
5151     in global1x1_tot/code_seaice_adj to access indices 32, 33
5152     (worth another tag)
5153 edhill 1.524
5154 jmc 1.1203 checkpoint57n_post (2005/07/29)
5155 heimbach 1.521 o adding precip control xx_precip 32
5156     o adding swflux control xx_swflux 33
5157 heimbach 1.522 o Replacing 10 forcing penalty cost routines by 1 generic.
5158     o Implementing partitioning in time-mean and variable adjustment
5159     for atmos. state.
5160     o Time-mean constant error is now read in data.ecco (instead of hard-coded)
5161 heimbach 1.519 o in natl_box_adjoint:
5162 heimbach 1.522 * updated exp 1 to 10
5163     (but does not have time-mean vs. variable split results yet)
5164 heimbach 1.523 o updated global1x1/*_seaice_adj/
5165     to incorporate latest changes
5166 heimbach 1.520 o enable useSingleCpuIO for mdsio vector routines
5167     (applies in particular to tapelev I/O)
5168     o removed inefficient K-loop in all active_file*control*.F
5169 heimbach 1.518
5170 jmc 1.1203 checkpoint57m_post (2005/07/28)
5171 jmc 1.516 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
5172     and advect_cs (use EXCH-2 and standard cs-32 grid files).
5173 jmc 1.515 o pkg/exch2: filling of face-corner halo regions is optional
5174     (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
5175    
5176 jmc 1.1203 checkpoint57l_post (2005/07/14)
5177 jmc 1.514 tag before updating tutorials (pre-release-2)
5178 jmc 1.513 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
5179     for output and interpolation of input fields onto model grid)
5180     o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
5181     Affects results of exp. rotating_tank ; update output.txt.
5182 jmc 1.511 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
5183 jmc 1.512 and taking the square quantity and/or using a fraction-weight field.
5184 jmc 1.511 o fix aim_diagnostics_init.F mate numbers.
5185     o add mnc output capability to diagnostics/diagstat and update
5186 edhill 1.510 our cvsignore files for the ACSII output generated
5187    
5188 jmc 1.1203 checkpoint57k_post (2005/07/02)
5189 heimbach 1.509 o lab_sea now uses diagnostics package and provides a suite of
5190     new EXF diagnostics output.
5191    
5192 jmc 1.1203 checkpoint57j_post (2005/06/30)
5193 heimbach 1.508 o exf
5194     * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
5195     Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
5196     terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
5197     * extended diagnostics output
5198     - now includes all EXF variables
5199     - hs, hl moved to common block
5200     - separate S/R for diagnostics, called after ctrl vector is added
5201     - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
5202     - EXFqnet contains true Qnet (i.e. includes qsw)
5203     * updated verif. lab_sea, global_with_exf
5204     * Rearranging hflux (exf_mapfields -> exf_getforcing)
5205     to ensure that diagnostics sees a true EXFqnet
5206 jmc 1.507 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
5207 jmc 1.506 o diagnostics pkg: change pointers so that 1 diagnostic can be used
5208     several times with different frequencies.
5209 edhill 1.505 o mnc-ify the thsice package as requested by Daniel Enderton
5210     - the monitor--MNC output needs work
5211     - many attributes need to be added (most are currently blank)
5212     o mnc-ify theaim_v23 package as requested by Daniel Enderton
5213     - many attributes need to be added (most are currently blank)
5214 jmc 1.503 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
5215 jmc 1.502 o add Sadourny like discretization to the 4th.O vorticity advection scheme
5216 jmc 1.500 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
5217 jmc 1.501 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
5218     fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
5219 jmc 1.499 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
5220     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
5221    
5222 jmc 1.1203 checkpoint57i_post (2005/06/19)
5223 molod 1.497 o Diagnostics package was changed: diagnostic allocation is now deactivated
5224     by setting an empty file name in the namelist (used to be by setting 0 frequency)
5225 jmc 1.496 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
5226     add 1rst Order upwind vertical Shear.
5227 edhill 1.495 o add a quick fix for A/B checkpointing in OFFLINE mode
5228 edhill 1.494 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
5229     end-run around the C/Fortran linking horror in eesup/src/timers.F
5230 adcroft 1.493 o added pkg/runclock: allows user to terminate run based on wall clock
5231     o added non-hydrostatic scaling parameter: nh_am2
5232 mlosch 1.492 o pkg/my82: futile attempt to make results compiler-independent by adding
5233     some "_d 0", etc. no effect.
5234 edhill 1.491 o for mnc output, fill the 'T' coordinate var with myTime and create a
5235     separate 'iter' variable for iteration count
5236 jmc 1.489 o pkg/diagnostics:
5237 jmc 1.490 add new capability: output of Global/Regional & per-level statistics ;
5238     tested against monitor output (including land & thSIce) on various exp.
5239     o make seaice-pkg I/O type flags (MNC/MDS) more standard.
5240 jmc 1.489
5241 jmc 1.1203 checkpoint57h_done (2005/05/19)
5242 jmc 1.488 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
5243     data.diagnostics, data.gchem, data.ptracers) is done.
5244    
5245 jmc 1.487 o pkg/diagnostics: prepare for Global/Regional statistics.
5246     add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
5247 jmc 1.486 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
5248     and rename it: DIFFERENT_MULTIPLE
5249    
5250 jmc 1.1203 checkpoint57h_post (2005/05/14)
5251 jmc 1.485 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
5252 jmc 1.484 o pkg/diagnostics: change output frequency, now in seconds (instead
5253     of Nb of iterations). This requires to change data.diagnostics.
5254 jmc 1.1203 checkpoint57h_pre (2005/05/12)
5255 jmc 1.483
5256 edhill 1.482 o in mnc, let the user create the output dir if both mnc_outdir_date
5257     and mnc_outdir_num are false
5258 edhill 1.481 o add fflags() to pkg/diagnostics which allows one to specify, on a
5259     per-file basis, the file precision [default behavior is unchanged]
5260 dimitri 1.480 o added diagnostics to pkg/kpp, including computation of mixed layer
5261     depth based on a temperature/density criterion
5262     o updated verification/natl_box to test the new pkg/kpp diagnostics
5263 jmc 1.479 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
5264 jmc 1.478 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
5265 edhill 1.477 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
5266     not mnc -- this mistake was found by JMC and is now corrected
5267    
5268 jmc 1.1203 checkpoint57g_post (2005/04/15)
5269 jmc 1.476 o add Adams-Bashforth 3rd Order time stepping:
5270     - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
5271     - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
5272 jmc 1.1203 checkpoint57g_pre (2005/04/15)
5273 jmc 1.475
5274 heimbach 1.472 o make lambda[Theta,Salt]ClimRelax spatially varying
5275     (default remains spatially uniform constant based on tau)
5276 heimbach 1.473 o added new control variables
5277     * init. uVel, vVel, etanN
5278     * lambda[Theta,Salt]ClimRelax
5279     o separate masks used for ctrl_pack/unpack 'from write_grid' output
5280     (suggested by G. Forget)
5281 heimbach 1.472
5282 jmc 1.1203 checkpoint57f_post (2005/04/06)
5283 jmc 1.471 o add parameter "baseTime" = model base time = time at iteration zero
5284     new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
5285     account for baseTime shift
5286     o move Coriolis arrays from PARAMS.h to GRID.h
5287 jmc 1.1203 checkpoint57f_pre (2005/04/06)
5288 jmc 1.470
5289 edhill 1.468 o mnc-ifying the seaice package
5290 adcroft 1.467 o introduced an alternative length scale calculation for use in the limiting
5291     maximum viscosity (off by default, see mom_vi_hdissip.F for details)
5292 heimbach 1.466 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
5293 baylor 1.465 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
5294     as well as grad(vort3). Made it compatible with both approximate form
5295     for the cubed sphere and full form of these gradients. Added flag
5296     useFullLeith to select between approximate and full form.
5297 jmc 1.464 o add "d0" in getcon.F to reduce differences between compilers/platforms
5298     update output.txt of exp. fizhi-gridalt-hs
5299 jmc 1.463 o change port_rand funtion to allow to set the seed.
5300 edhill 1.462 o fix obscure MNC bug involving conversion between reals and integers
5301     - it caused no problems with certain (eg. gcc, ifc) compilers but the
5302     new version is now more standards-compliant
5303 heimbach 1.469 o adjoint-related modifications
5304     * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
5305     * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
5306     * mom_vi_hdissip: to be able to use Leith scheme in adjoint
5307 edhill 1.462
5308 jmc 1.1203 checkpoint57e_post (2005/02/28)
5309 heimbach 1.461 o Adding eddy stress controls a la Ferreira et al.
5310 jmc 1.474 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
5311 heimbach 1.460
5312 jmc 1.459 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
5313     update output.txt of exp. fizhi-gridalt-hs
5314 edhill 1.458 o add more "Z" dimensions and associated coordinate vars to MNC
5315 dimitri 1.457 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
5316 dimitri 1.456 o parameter calendarDumps: when set, approximate months (30-31 days) and years
5317     (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
5318     KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
5319     months and years. Requires pkg/cal.
5320 edhill 1.455 o diagnostics: add pickup functionality
5321     - off by default for backwards compatibility
5322     - current version only uses MDSIO -- MNC will be added
5323 jmc 1.454 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
5324 jmc 1.452 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
5325    
5326 jmc 1.1203 checkpoint57d_post (2005/02/11)
5327 jmc 1.451 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
5328 edhill 1.450 o modify verification/ideal_2D_oce so that it tests the creation of mnc
5329     output from the diagnostics package
5330 jmc 1.449 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
5331 edhill 1.448 o make genmake2 more portable by using ".$FS" instead of ".f" for more
5332     of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
5333 edhill 1.447 o add coordinate variables to the MNC output from the diagnostics package
5334 jmc 1.446 o change MNC-flags default value: true when useMNC=TRUE
5335 edhill 1.444 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
5336     the ability (off by default) to read the grid information using MNC
5337 jmc 1.445 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
5338 jmc 1.443 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
5339 jmc 1.442 o do snap-shot diagnostics at the middle of the time-interval (instead of
5340     at the end).
5341 jmc 1.441 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
5342     new test for AIM with thSIce + slab-ocean
5343 jmc 1.440 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
5344 jmc 1.439 o move state variable diagnostics to the beginning of the time step ;
5345     (note: still needs some work specially for snap-shot diagnostics)
5346     duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
5347    
5348 jmc 1.1203 checkpoint57c_post (2005/01/27)
5349 jmc 1.438 o Change testing option (-ieee) to get closer agreement between g77 & ifort
5350     o generate new output.txt files on faulks with g77 & the new -ieee option
5351 jmc 1.1203 checkpoint57c_pre (2005/01/27)
5352 jmc 1.437
5353     o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
5354 jmc 1.436 update output.txt of exp. global_ocean.90x40x15
5355 jmc 1.435 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
5356     results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
5357 jmc 1.432 o add saltFlux(+File) forcing capability with periodicExternalForcing
5358 jmc 1.431 o allow to use pkg diagnostics for GM-Redi & ThSIce output
5359     o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
5360 edhill 1.430 o improvements for the MNC output from DIAGNOSTICS:
5361     - correct handling of the unlimitied dimension
5362     - all dims now have associated coordinate variables
5363     - variables located at U, V, and Corner ("Z") points are now written
5364     with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
5365     *all* data points are output
5366 dimitri 1.429 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
5367 dimitri 1.428 o added pkg/seaice/seaice_monitor.F
5368 dimitri 1.427 o mdsio_readfield.F can now read files visible only to master MPI process.
5369 dimitri 1.426 o pkg/seaice: some test code for ice-modified ocean stress
5370 dimitri 1.425 o exf_getffields interpolation defaults to bilinear for all scalar forcing
5371     fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
5372     spurious negative numbers for precipitation and humidity. Will cause
5373     some small numerical differences for integrations using pkg/exf/exf_interp.F.
5374 heimbach 1.434 o pkg/ctrl/
5375     * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
5376     May be enabled via doPackDiag
5377     * introduce z-scaling of
5378     + gradient (doZscalePack) and
5379     + control (doZscaleUnpack)
5380     o pkg/mdsio/
5381     * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
5382     * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
5383 dimitri 1.425
5384 jmc 1.1203 checkpoint57b_post (2004/12/20)
5385 jmc 1.424 o simplify options in diagnostics_fill arguments (remove weird combinations)
5386 edhill 1.423 o fix MNC coordinate variables so that they now contain per-face index
5387     values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
5388     general, EXCH2 grids are only aligned to a "local" coordinate system
5389 jmc 1.422 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
5390     o Implement instantaneous output within pkg diagnostics:
5391     setting a negative frequency in data.diagnostics produces
5392     "snap-shot" output (as opposed to time-average if freq > 0)
5393 jmc 1.421 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
5394     NOTE: change ptracer diagnostics name: use 2 characters to work with
5395     more than 9 tracers. Add also diagnostics of advect & diffus flux.
5396 edhill 1.420 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
5397     becomes the coordinate variable for the 'T' dimension
5398 edhill 1.419 o add CF-style coordinate variables to MNC
5399     - just a first cut: numbers are meaningless on the cubesphere and
5400     missing along the T axis but otherwise it works!
5401 dimitri 1.418 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
5402 jmc 1.417 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
5403 jmc 1.416 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
5404     this is based directly on what the model compute, so that the content of
5405     each diagnostics might be affected by switching options (e.g., implicitDiffusion)
5406     o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
5407 mlosch 1.415 o clean up build options files for SunOS, in particular
5408     - remove -traditional from xmakedepend
5409     - change -xarch=v9 to -xarch=native for f77
5410     - restore use of make (not gmake)
5411     - add CC=gcc if using g77
5412 edhill 1.413 o changes per discussion of AM, JMC, & EH3 today:
5413     - move redundant "grid" variables out of "state" -- in preparation of
5414     creating proper CF-style coordinate variables and in recognition
5415     that any/all grid variables can be easily copied (eg. w/NCO) from
5416     the grid files into any of the other NetCDF files
5417     - *always* output grid variables with MDSIO (this will eventually be
5418     changed)
5419     - output MNC grid file if useMNC is true
5420 edhill 1.412 o every instance of _END_MASTER() has been found and replaced with
5421     _END_MASTER( myThid ) in order to satisfy certain picky Sun
5422     preprocessors
5423 jmc 1.411 o re-arrange diagnostics pkg initialisation:
5424     - allow each package to extend the available diagnostics list
5425     - add some checking and fix small problems (multi-threaded, ...)
5426     - new S/R diagnostics_fill (replace fill_diagnostics):
5427     look through the short list of active diag. (instead of the long list)
5428     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
5429 edhill 1.381
5430 jmc 1.1203 checkpoint57a_post (2004/12/10)
5431 heimbach 1.410 o this set of changes restores TAMC compatibility
5432     tested for global_ocean.90x40x15 adjoint on trough
5433     (what a pain)
5434    
5435 jmc 1.1203 checkpoint57a_pre (2004/12/10)
5436 heimbach 1.409 o some modifs in tools/build_options for sunos
5437     o call ctrl_pack for ctrl at end for optimcycle=0
5438    
5439 jmc 1.1203 checkpoint57 (2004/12/09)
5440 mlosch 1.406 o add horizontal bi-harmonic viscosity for vertical velocity
5441     - new parameter viscA4W (defaults to viscA4)
5442     - affects only non-hydrostatic code
5443     - to be done: no-slip lateral boundary conditions
5444 dimitri 1.405 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
5445 jmc 1.404 o implement Implicit Vertical advection for pTracers
5446 jmc 1.401 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
5447 jmc 1.402 (implemented also for implicit vertical diffusion & advection)
5448 mlosch 1.400 o OBCS: extend application of tracer open boundary conditions
5449     to a strip beyond the boundary of width Olx/Oly
5450 heimbach 1.403 o add call monitor to TAF set of required calls (flow directives)
5451     and include in natl_box_adjoint
5452     o untangle a few ifdefs related to cost, ctrl, autodiff
5453     untangel a few ALLOW_ECCO_OPTIMIZATION
5454 heimbach 1.407 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
5455     (theta2, salt2 in ecco_cost_weights)
5456 mlosch 1.400
5457 jmc 1.1203 checkpoint56c_post (2004/12/03)
5458 mlosch 1.399 o OBCS as control variables
5459     - update ctrl_ad_diff.list, obcs_ad_diff.list
5460     - remove balance of obcs controls from default
5461     - fix index bug nobcs in ctrl_init
5462     - fix dummy fields filen in ctrl_pack
5463     - add dummy weights for obcs
5464     o lsopt: comment out fort.94 output
5465     o optim:
5466     - remove unnecessary header files
5467     - adjusted namelists
5468     - add xerbla.F to Makefile
5469     o exf:
5470     - multiple modifications of exf_check_range
5471     - unit change in exf_init_runoff from [m/year] to [m/s]
5472     o mdsio:
5473     - i/o-vector change debugLevel from debLevA to debLevB
5474    
5475 jmc 1.1203 checkpoint56b_post (2004/12/01)
5476 mlosch 1.397 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
5477     is called from DO_THE_MODEL_IO
5478     - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
5479     - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
5480     - clean up PTRACERS_WRITE_TIMEAVE a little
5481 mlosch 1.396 o add another verification experiment that tests both the cfc-pkg and
5482     the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
5483     reactive tendencies treated inline with regular timestepping
5484 mlosch 1.395 o testreport previously did a lousy job of comparing small numbers, so
5485     we (Ed and Martin) changed the way the cut-off of 1.e-12 is
5486     implemented in the little c-progam tmp_cmpnum.c which is embedded in
5487     testreport.
5488     o ptracers_monitor: bug fix for MPI
5489    
5490 jmc 1.1203 checkpoint56a_post (2004/11/28)
5491 mlosch 1.394 o GCHEM: finish reorganizating the package
5492     - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
5493     (introduces another 3D-array for each passive tracer, but only if
5494     GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
5495     gchemTendency is not needed because the timestep is done separately)
5496     - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
5497     - GCHEM is now---more or less cleanly---separate from PTRACERS
5498     - to bo done: handling of surfaceForcingPtr that is needed for KPP not
5499     so clear to me how that should be done in a general way.
5500     o CFC: improve formatting of output in CFC_ATMOS
5501     o PTRACERS:
5502     - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
5503     that ALL experiments with ptracers enable can be checked. This makes
5504     GCHEM_MONITOR obsolete.
5505     - include a runtime parameter PTRACERS_monitorFreq that defaults to
5506     monitorFreq
5507     - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
5508 edhill 1.393 o add PTRACERS (PTR0[1-5]) to testreport output
5509 heimbach 1.391 o exf_check_range:
5510     * default changed to .TRUE.
5511     * will check values for niter0 if debLevA, every timestep if debLevB
5512     * STOP in exf_check_range if 'out of range'
5513     * range chosen generous to allow for potential extema
5514     TBD: a version with stricter range
5515     permitted range would be runtime parameters
5516 jmc 1.390 o GMredi:
5517     - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
5518     - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
5519     - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
5520 mlosch 1.388 o GCHEM:
5521     - move call to GCHEM_FORCING_SEP, so that it is now called before
5522     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
5523     - introduced a useGCHEM runtime flag and applied it everywhere.
5524 mlosch 1.392 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
5525     this flag is now only visible within GCHEM-pkg routines.
5526     - moved gchem_forcing_int temporarily into ptracers_forcing, this will
5527     be replaced by a 3D array that is computed before thermodynamics; for
5528     this, the tracer ID iTracer had to be included into the parameter list
5529     of ptracers_forcing
5530 mlosch 1.394 - set up forward_step to call gchem_forcing, that will replace
5531 mlosch 1.392 gchem_forcing_int in ptracers_forcing
5532     - cleaning up
5533 jmc 1.389 o small cleaning of exch2: remove files that are also in eesupp/src
5534 mlosch 1.387
5535 jmc 1.1203 checkpoint56 (2004/11/17)
5536 jmc 1.385 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
5537 edhill 1.384 o mnc: cleanup "full" files--fixes out-of-memory problem
5538 heimbach 1.386 o ECCO-GODAE
5539     * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
5540     * fully merged and updated from SIO code
5541     windstress sign change affects
5542     - exf_inscal_[u/v]stress
5543     - sign of xx_tau[u/v] adjustments
5544     - signs in cost_scat
5545     * ctrl_get_gen: avoid update of tau[u/v] for first few days
5546     * natl_box_adjoint updated and compressed
5547     * 2-level checkpoint switch added
5548     (tested in EXP. 1 of natl_box_adjoint)
5549     * new switch doInitXX to avoid init. of xx_... in optimcycle=0
5550     o SVD
5551     * first complete, non-hacked version for SVD calculations
5552     * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
5553     performed via direct access files admtlm_vector.it????
5554     (via ctrl_[un]pack)
5555     * optimcycle is used for ARPACK iteration counter
5556     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
5557     * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
5558     and add linear transforms where necessary
5559     * controls are initial/final SST, SSS (can be extended; need to check
5560     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
5561     o mdsio: filename info to both stderr, stdout
5562     o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
5563     from sign change
5564 edhill 1.384
5565 jmc 1.1203 checkpoint55j_post (2004/11/10)
5566 jmc 1.382 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
5567     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
5568 edhill 1.381 o add consistent build directories and .cvsignore files to verification
5569 dimitri 1.380 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
5570 edhill 1.379 o make all subroutines 30 or less characters in length for certain older
5571     compilers to work (a thorough search only turns up two routines in
5572     pkg/ptracers)
5573 jmc 1.378 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
5574     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
5575    
5576 jmc 1.1203 checkpoint55i_post (2004/10/28)
5577 jmc 1.376 o change arrays for total vertical diffusivity (2.D if explicit,
5578     3.D if implicit) ; each ptracer uses its own background value.
5579 edhill 1.375 o added mnc/NetCDF output capability to ocn_compon_interf
5580     - added bits to verification/cpl_aim+ocn so that it can run on
5581     ITRDA and other clusters without the mpirun "-wd" option
5582 afe 1.374 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
5583     configuration
5584 edhill 1.373 o give MNC the ability to create additional files rather than
5585     exceeding a specified file size limit "MNC_MAX_FILESIZE"
5586     - the default is just less than 2GB which is a practical limit
5587     on many systems
5588 jmc 1.372 o Compute the non-local term using either KPP vertical diffusivity (=default)
5589     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
5590 jmc 1.349
5591 jmc 1.1203 checkpoint55h_post (2004/10/20)
5592 jmc 1.371 o add verification test "vermix"
5593 edhill 1.370 o remove all the *_ioinc flags and replace with the single global
5594     outputTypesInclusive flag
5595 jmc 1.369 o allow to set a vertical profile of vertical diffusivity for T & S
5596 jmc 1.371 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
5597     o useMNC moved from data.mnc to data.pkg
5598 jmc 1.369
5599 jmc 1.1203 checkpoint55g_post (2004/10/14)
5600 heimbach 1.368 o Renaming carbon AD experiments to comply with testreport conventions
5601     o Updating adjoint of Held-Suarez hs94.1x64x5
5602     o Fixing directives for non-ECCO forward_step, after ECCO directives
5603     have been fixed to avoid recomp. of do_oceanic_phys
5604     Works well for global_ocean.90x40x15,
5605     but recomp. issue remains for carbon
5606     o Updating adjoint output for natl_box_adjoint after
5607     pkg/ecco has been modified (see taga c55d_post)
5608    
5609 jmc 1.1203 checkpoint55f_post (2004/10/13)
5610 edhill 1.367 o rename to timeave_init_fixed
5611    
5612 jmc 1.1203 checkpoint55e_post (2004/10/13)
5613 heimbach 1.366 o some delicate re-shuffle of store directives to avoid one
5614     extra call of do_oceanic_physics
5615     affects ecco_the_main_loop.F, do_oceanic_physics.F
5616     checkpoint_lev1_directives.h
5617     o NB: this may break global_ocean adjoint temporarily,
5618     but it is clear how to fix it. Will do later, need this now.
5619    
5620 jmc 1.1203 checkpoint55d_post (2004/10/11)
5621 heimbach 1.365 o ECCO specific cost function terms (up-to-date with 1x1 runs)
5622     o ecco_cost_weights is modified to 1x1 runs
5623     o modifs to allow observations to be read in as
5624     single file or yearly files
5625     o enable to read exf forcing fields as either
5626     single file or yearly files (flag useExfYearlyFields)
5627 jmc 1.1203 checkpoint55d_pre (2004/10/08)
5628 heimbach 1.365
5629     o switch between 2-level and 3-level checkpointing
5630 edhill 1.364 o add ability of MNC to write local and "partial" (eg. 2D slices where
5631     the full 3D field is never actually stored) arrays to NetCDF files
5632     with the correct (that is, the complete multi-dimensional) set of
5633     array indicies
5634     - used in mom_vecinv() to write the diagFreq output
5635     - tested (demonstrated) in verification/aim.5l_cs
5636 edhill 1.363 o further mnc-ification
5637     - add verification/lab_sea to the list with mnc setups
5638     - fix undefined mnc v-names in cd_code
5639     - add kpp to mnc output (both snapshot and timeave)
5640 mlosch 1.362 o non-hydrostatic code
5641     - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
5642     in calc_gw.F
5643     - defaults to viscAh
5644     - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
5645     friction or Leith) in non-hydrostatic mode, as long as there is
5646     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
5647 heimbach 1.360 o pkg/cost
5648     extend simple cost functions to treat time mean quantities
5649     (T,U,V) via cost_accumulate_state from cost_tile
5650 jmc 1.358 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
5651     be 2 times larger than the minimum size the advection scheme requires.
5652     now get a perfect conservation of salt in advect_cs test-exp (updated)
5653 mlosch 1.356 o GGL90 (Gaspar's TKE mixed layer)
5654     - add horizontal diffusion of TKE, requires exchanges in
5655     do_fields_blocking_exchanges, horizontal diffusivity is zero by
5656     default. In OPA there is no horizontal diffusion of TKE but the
5657     mixing coefficients are computed from a horizontal average of TKE of
5658     6 points or so. I think that diffusion has a little more physical
5659     justification.
5660     - clean up ggl90_calc in the hope of reducing memory usage (this hope
5661     was in vain)
5662     - mask tke-variable in ggl90_init
5663 jmc 1.355 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
5664     o fix biharmonic diffusion on CS-grid.
5665 mlosch 1.354 o more obcs stuff
5666     - added obcs_external_fields_load as an alternative to the EXF-pkg option
5667     for reading boundary values. This routine is called from
5668     obcs_prescribe_read
5669     - updated obcs_check
5670 mlosch 1.357 - changed sponge layer relaxation parameter units for days to seconds
5671     - turned off sponge layer by default
5672 heimbach 1.359 - changed argument list of OBCS_CALC to myTime+deltaTclock
5673 mlosch 1.361 - fixed about 35 bugs in obcs_external_fields_load
5674 mlosch 1.354
5675 jmc 1.1203 checkpoint55c_post (2004/09/23)
5676 heimbach 1.352 o obcs stuff
5677     - new runtime flags useOBCSprescribe, useOBCSbalance
5678     - re-arranged obcs_calc
5679     - moved exf_getobcs to obcs_prescibe_read
5680     obcs_prescibe_read is called after ORLANSKI stuff
5681     and independent of it (executable can contain all).
5682     - updated obcs_check
5683 heimbach 1.353 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
5684     These may be necessary only if tangential velocities are
5685     prescribed at OB, not sure, needs testing.
5686 edhill 1.351 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
5687     which simplifies the calls and passes the ifc check-bounds test
5688    
5689 jmc 1.1203 checkpoint55b_post (2004/09/22)
5690 jmc 1.350 o add a 2D scalar, Z location, exchange_2 routine.
5691 jmc 1.349 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
5692     to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
5693     affects advect_cs results (for the wrong reason): update output.txt
5694 jmc 1.348 o use a more standard discretization for biharmonic viscosity ;
5695     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
5696     affects results of dome set-up: update output.txt
5697     o fix gad_advection.F (CubedSphere part), back to version 1.23
5698     o fix bug in mom_vi_del2uv.F (CubedSphere part).
5699 mlosch 1.341
5700 jmc 1.1203 checkpoint55a_post (2004/09/20)
5701 heimbach 1.347 o merged code to
5702     * prescribe/read time-dependent open boundaries
5703     (works in conjunction with exf, cal)
5704     * sponge layer code for open boundaries
5705     * each boundary N/S/E/W now has its own CPP option
5706     (healthy for the adjoint)
5707    
5708 jmc 1.1203 checkpoint55 (2004/09/17)
5709 heimbach 1.346 o up-to-date adjoint of previous breaks
5710     - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
5711     - global_ocean_ebm: adjoint still needs fix (TLM ok)
5712     - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
5713     - carbon: * remove tr1-related adjoint verification
5714     * add ptracer as control variable
5715     o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
5716     (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
5717    
5718 jmc 1.1203 checkpoint54f_post (2004/09/16)
5719 heimbach 1.345 o in verification/carbin/ remove experiment related to
5720     ALLOW_PASSIVE_TRACER (array tr1 etc)
5721     code_ad/ input_ad/ results_ad
5722    
5723 mlosch 1.344 o add two new packages
5724     - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
5725     + subject to optimization (memory)
5726     - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
5727     + subject to reordering (many GOTOs in the original code)
5728     + so far opps is called for every (i,j) point, and then operates in
5729     the vertical; one may want to reorder the scheme in order operate in
5730     horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
5731     fields)
5732 edhill 1.343 o overhaul of IO so that we now have flags for MDSIO and/or MNC
5733     - all verification tests compile and run with linux_ia32_g77
5734     - defaults are compatible with current input files--nothing
5735     should change if you were not previously using MNC
5736     - MNC output has been added in numerous places (eg. timeave)
5737     but there are still a few writes not yet do-able with MNC
5738     (this is in progress)
5739     - flags now allow for either/or/both use of MDSIO and MNC and
5740     documentation will soon follow
5741     - numerous small formatting cleanups for ProTeX
5742 edhill 1.342 o add version info (via BUILD_INFO.h) to MNC and stdout
5743    
5744 jmc 1.1203 checkpoint54e_post (2004/09/02)
5745 mlosch 1.341 o add two new packages
5746     - pp81 (Packanowski and Philander, 1981), Richardson number and
5747     stratification dependent mixing
5748     - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
5749     - these scheme operate in a similar manner as KPP (without ghat, of
5750     course), however there is only one diffusivity that is used for both
5751 mlosch 1.1068 temperature and salinity (and passive tracers)
5752 stephd 1.340 o add offline package
5753 edhill 1.339 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
5754     provided by Stephanie Dutkiewicz
5755 edhill 1.338 o genmake2: add ability to search for C compilers and cleanup test output
5756     - fixes recent SX-6 problems and should help with others (eg. HP-UX)
5757    
5758 jmc 1.1203 checkpoint54d_post (2004/07/27)
5759 adcroft 1.336 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
5760 jmc 1.337 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
5761     leading to additional shift by 5 days each year of integration
5762     (i.e. leading to considerable offset over the years)
5763 jmc 1.335 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
5764     o start with no AB and no initial filtering (staggerTimeStep):
5765     change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
5766     o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
5767     (external loading & cpl import/export stay in forward_step.F)
5768     o update coupling interface to work with new staggerTimeStep
5769     o change MDSIO ptracers_pickup.
5770 jmc 1.334 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
5771 edhill 1.333 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
5772 jmc 1.334 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
5773 edhill 1.333
5774 jmc 1.1203 checkpoint54c_post (2004/07/18)
5775 jmc 1.331 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
5776     this affects (truncation error) output.txt of test-exp:
5777     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
5778     o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
5779 jmc 1.330 o change Qnet to always be the net heat flux, (+upward).
5780     affects (truncation error) output of natl_box exp.: updated
5781 jmc 1.329 o define the max number of passive tracers in PTRACERS_SIZE.h
5782     o start to test mnc routinely in exp0
5783     o add sea-ice loading (sIceLoad) as a new forcing field.
5784    
5785 jmc 1.1203 checkpoint54b_post (2004/07/08)
5786 edhill 1.327 o add testreport "-j JOBS" option for parallel builds (tested and pretty
5787     impressive on Altix and Opteron systems)
5788 edhill 1.326 o diagnostics can now write NetCDF files through the mnc package
5789 jmc 1.325 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
5790 jmc 1.324 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
5791 jmc 1.323 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
5792     affects (truncation error) output of lab_sea & natl_box exp.: updated
5793     o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
5794    
5795 jmc 1.1203 checkpoint54a_post (2004/07/06)
5796 jmc 1.322 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
5797     o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
5798     o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
5799     o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
5800     + internal_wave (shift in writing cg2d_ini_res)
5801 jmc 1.1203 checkpoint54a_pre (2004/07/05)
5802 jmc 1.321
5803 dimitri 1.320 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
5804     - modified verification/lab_sea and natl_box_adjoint accordingly
5805    
5806 jmc 1.1203 checkpoint54 (2004/07/02)
5807     checkpoint53g_post (2004/07/02)
5808 jmc 1.317 o prepare splitting of thermodynamics: store convect.counter in common block
5809 jmc 1.316 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
5810     output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
5811 dimitri 1.315 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
5812 jmc 1.314 o new parameter "nShapS": allow to treat differently S from T (nShapT)
5813     o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
5814 heimbach 1.318 o restore adjointability
5815 jmc 1.314
5816 jmc 1.1203 checkpoint53f_post (2004/06/25)
5817 jmc 1.313 o modifications that affect AIM experiment results (update output.txt):
5818     - no advection of S at top interface Nr (pkg/generic_advdiff)
5819     - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
5820 jmc 1.312 o AIM pkg:
5821     - include stability function into surf.Flux derivative relative to Tsurf
5822     - calculate clear-sky radiation & surface temp. change (for diagnostics)
5823 jmc 1.313
5824 afe 1.311 checkpoint53e_post
5825     o merged cylindrical coord configuration
5826     o added rotating_tank experiment
5827 afe 1.310 checkpoint53e_pre
5828    
5829 jmc 1.1203 checkpoint53d_post (2004/06/14)
5830 jmc 1.308 o faulks upgraded: re-generate output.txt that have changed:
5831     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
5832 adcroft 1.307 o Added Bryan and Lewis, 1979, vertical diffusivity profile
5833 jmc 1.306 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
5834 adcroft 1.305 o added Sadourny discretization of Coriolis
5835     - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
5836     - re-enabled use of omega3 (useAbsVorticity)
5837 adcroft 1.304 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
5838 jmc 1.309 vector-invariant equations
5839 adcroft 1.304 - note: does *NOT* yet use same variable visc. for no-slip BC's.
5840 mlosch 1.303 o recoded the lateral boundary conditions for non-hydrostatic w, this time
5841     hopefully without new bugs
5842     - still to do: biharmonic friction for non-hydrostatic w
5843 adcroft 1.302 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
5844     o regenerated output for global_ocean_ebm (using -ieee)
5845 adcroft 1.301 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
5846     of mom_common/
5847     - simple re-arrangement of instructions within computing loop
5848 jmc 1.1203 checkpoint53d_pre (2004/05/21)
5849 mlosch 1.297
5850 jmc 1.1203 checkpoint53c_post (2004/05/21)
5851 jmc 1.299 o new version of coupler for AIM+thSIce and Ocean models
5852     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
5853     - land: change Evaporation of snow
5854     - aim with thSIce: fix bug in snow-precip.
5855 mlosch 1.297 o changes to calc_gw.F
5856     - bug fix for w^2 term near the bottom boundary
5857     - (hopefully) improve the lateral slip boundary condtions for use with
5858     partial/looped cells
5859     - because the bug fix changes two verification experiments anyway (exp5
5860     and plume on slope), change the lateral boundary condition from half slip
5861     to the value of no_slip_sides
5862 heimbach 1.298 o ebm package wasnt quite up to the parallel task. Fixed that.
5863 heimbach 1.300 o Adjoint of EBM package + verification
5864     * TLM OK
5865     * ADM not sufficient accuracy yet (needs further testing)
5866 heimbach 1.295
5867 jmc 1.1203 checkpoint53b_post (2004/05/14)
5868 heimbach 1.296 o Commiting new energy balance model to repository
5869     * package is pkg/ebm
5870     * verif. is verification/global_ocean_ebm
5871     * references are in ebm_driver.F
5872     C * X. Wang, P. Stone and J. Marotzke, 1999:
5873     C Global thermohaline circulation. Part I:
5874     C Sensitivity to atmospheric moisture transport.
5875     C J. Climate 12(1), 71-82
5876     C * X. Wang, P. Stone and J. Marotzke, 1999:
5877     C Global thermohaline circulation. Part II:
5878     C Sensitivity with interactive transport.
5879     C J. Climate 12(1), 83-91
5880     C * M. Nakamura, P. Stone and J. Marotzke, 1994:
5881     C Destabilization of the thermohaline circulation
5882     C by atmospheric eddy transports.
5883     C J. Climate 7(12), 1870-1882
5884     o Will need long integration testing.
5885 jmc 1.1203 checkpoint53b_pre (2004/05/14)
5886 dimitri 1.292
5887 adcroft 1.294 o created pkg/mom_common in preparation for variable viscosity code
5888     o renamed and split ini_mnc_io
5889 jmc 1.293 o pkg/land: only liquid water can diffuse or run-off
5890     o AIM using land: soil wetness availability account for snow
5891 dimitri 1.292 o added printMapIncludesZeros to EEPARMS namelist
5892 heimbach 1.290
5893 jmc 1.1203 checkpoint53a_post (2004/05/11)
5894 heimbach 1.290 o restore TAMC compatiility for exf_constants.h
5895     (no usage of _d in .h)
5896     o Additional storing in KPP in an attempt to fix
5897     TAMC problem with adjoint of KPP code.
5898     (no success...)
5899     Identical code works fine with TAF.
5900 dimitri 1.291 o Fixed verification/natl_box_adjoint experiments.
5901     Initial conditions for Experiments 4 and 5 are now
5902     set to "SEAICE_initialHEFF=0", which is more reasonable,
5903     and hence gives results closer to that of Experiment 2.
5904     Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
5905 cnh 1.289
5906 jmc 1.1203 checkpoint53 (2004/05/06)
5907 cnh 1.289 o stable checkpoint with up to date adjoint
5908     TLM tests only run for 1st grdchk at the moment. Its unclear if
5909     this is a code problem or a problem with resetting code for g_
5910     variables that is being autogenerated wrong.
5911     Otherwise:
5912     o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
5913     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
5914     are both still in chaos following their security messes.
5915 jmc 1.279
5916 jmc 1.1203 checkpoint52n_post (2004/05/06)
5917 edhill 1.288 o various build (mostly genmake2) changes including:
5918     - ability to build/run more easily within Cygwin and MacOS X
5919     - more complicated Makefiles with a stronger dependence on Gnu Make
5920 dimitri 1.285 o pkg/seaice modifications
5921 dimitri 1.287 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
5922     of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
5923     and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
5924 dimitri 1.285 - changed proxy for geostrophic velocity and updated
5925 dimitri 1.286 verification/lab_sea/results/* accordingly
5926 dimitri 1.285 - removed ADI dynamic solver from pkg/seaice
5927     - replaced all occurrences of 1/CSTICE or 1/CSUICE
5928     they caused a segmentation fault under certain circumstances
5929 mlosch 1.283 - removed unused field WATR
5930 mlosch 1.282 o bug fix in exf-package:
5931     - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
5932     now reflect that.
5933 mlosch 1.281 o small fixes in the cal-package:
5934     - set reference date to first of January for the 'model'-calendar
5935     - failing of cal_CheckDate in cal_FullDate now actually results in a
5936     warning
5937 mlosch 1.280 o small modifications in exf-package to increase flexibility:
5938     - change climtempfreeze from a constant to a runtime parameter that
5939     is specified in data.exf_clim (default = -1.9)
5940     - introduce runtime parameter windstressmax (default = 2.0) that is
5941     specified in data.exf
5942 jmc 1.279 o fix in pkg/thsice:
5943     - update Evap (Tsf changes) to be consistent with Latent heat flux
5944     - maintain snow precipitation unchanged (even if Tsf >=0).
5945     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
5946 edhill 1.272
5947 jmc 1.1203 checkpoint52m_post (2004/04/18)
5948 mlosch 1.277 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
5949     this does not change any of the results, because myIter=0 in swfrac always
5950     lead to jwtype=2 (the default anyway), but the call makes little sense
5951     as a default
5952 jmc 1.276 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
5953 jmc 1.275 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
5954     atmospheric model (AIM) to use it ; add a "slab ocean" component.
5955     o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
5956     o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
5957 dimitri 1.274 o extending useSingleCpuIO option to work with new exch2 I/O format
5958     - old-style, missing-tile I/O is still accessible by defining CPP
5959     option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
5960 edhill 1.273 o monitor package can write to NetCDF files and/or STDOUT
5961     o fix re-definition bug in MNC_GRID_INIT_ALL()
5962 edhill 1.272 o doc/api_reference added
5963     - a framework for building an API Reference Manual using all
5964     the "protex" comments embedded in the code
5965     - see pkg/generic_advdiff, pkg/mnc for examples
5966 edhill 1.269 o MNC:
5967     - make myThid the last argument for all subroutines
5968     - new default for the grid files: NO halos
5969 edhill 1.270 - add useMNC and other run-time flags
5970     - separate per-file-group handling of the unlimited dimension
5971     - early initialization of MNC w/ flags read at the eeboot stage
5972     and lookup tables set in initialize_fixed
5973     - write all MNC output to a freshly-created directory
5974 jmc 1.268 o thermodynamics sea-ice (thsice) is now tested with testreport.
5975     o test exp. advect_cs: use the standard cs32 grid ; update output.
5976 heimbach 1.271 o Added functionality to grdchk:
5977     pick global i,j,k position (or nearest wet) where to perform check.
5978 jmc 1.266
5979 jmc 1.1203 checkpoint52l_post (2004/03/11)
5980 jmc 1.267 o new land formulation:
5981     a) use ground enthalpy as prognostic variable to ensure exact
5982     energy conservation.
5983     b) account for water temperature and for latent heat of freezing
5984     in all processes (rain, run-off, ground storage)
5985     c) compute surface and ground temperature implicitly.
5986     o aim_v23 modification for new land model:
5987     a) Treat separately land / ocean / sea-ice surface fluxes
5988     to allow implicit computation of land & sea-ice surface temp.
5989     b) add snow precipitation.
5990 jmc 1.1203 checkpoint52l_pre (2004/03/11)
5991 jmc 1.266
5992 jmc 1.265 o fix problem (when 1 tile is empty) in min/max monitor.
5993     o fix bug in timeAve (u,vZetatave in common block)
5994 dimitri 1.264 o no restoring terms under ice for pkg/seaice
5995 dimitri 1.263 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
5996     o bug fix for pkg/seaice pickups
5997 edhill 1.262 o change MNC call locations and add coordinate attributes
5998 jmc 1.260 o mask vorticity at the corner ; affects global_ocean.cs output
5999     o fix ini_curvilinear_grid ; test CS experiments with mpi
6000 jmc 1.259 o aim.5l_cs: modify sea-ice fraction input file ; update output
6001 heimbach 1.261 o exf: Adding simple range check routine for exf fields after read
6002 adcroft 1.256
6003 jmc 1.1203 checkpoint52k_post (2004/02/23)
6004 adcroft 1.256 o removed top-level directory "diags"
6005     - we migrated these functions to pkg/timeave a long time ago
6006     o fixed bug introduced in pkg/monitor
6007 heimbach 1.257 o accuracy ctrlprec = 32 insuffient for gradient checks using
6008     averaged fields (I/O via cost_averages)
6009     -> use ctrl.h in active_file*.F to control I/O precision.
6010     o paramter list of CALL ADTHE_MAIN_LOOP
6011     o added initial do_the_model_io to ecco
6012     o set all ...Freq to zero after cost_final
6013     taveFreq, dumpFreq, pChkptFreq
6014 heimbach 1.258 o MAIN and ECCO differentiability restored
6015 heimbach 1.255
6016 jmc 1.1203 checkpoint52j_post (2004/02/18)
6017 heimbach 1.255 o fix nchklev in tamc.h for global_ocean...
6018     o Bringing flow and store directives up-to-date
6019     o Really weird thing!
6020     call do_the_model_io from the_main_loop with parameters
6021     starttime, niter0, instead of mytime, myiter, screws up the adjoint:
6022     TAF places a faulty re-call of initialise_varia
6023     after cost_final call which should not be there!
6024 jmc 1.1203 checkpoint52j_pre (2004/02/03)
6025 jmc 1.253
6026 afe 1.254 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
6027     error messages
6028 jmc 1.253 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
6029 afe 1.252 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
6030     debug output
6031 afe 1.251 o modfied mdsio_writefield.F to handle non-global files under exch2
6032 jmc 1.250 o update AIM Cubed-Sphere exp (aim.5l_cs):
6033     use land, p*, and Franco.M forcing fields with fractional land-sea mask.
6034     o update AIM Equatorial Channel exp:
6035     use standard aim_v23 pkg and change the SST fields to be more realistic.
6036 afe 1.248 o globalFile now works with exch2
6037 afe 1.247 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
6038 jmc 1.253 mon_vort3.F to make exch2 friendly with >1 tile per cube face
6039 dimitri 1.249 o limit timeave output for hi-res integrations
6040 adcroft 1.245
6041 jmc 1.1203 checkpoint52i_post (2004/01/21)
6042 adcroft 1.245 o removed CPP_EEOPTIONS.h from verification/*/code
6043     o updated the tiling for global_ocean_pressure
6044 jmc 1.1203 checkpoint52i_pre (2004/01/20)
6045 jmc 1.246
6046     o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
6047     the old pkg/aim).
6048 afe 1.239
6049 jmc 1.1203 checkpoint52h_pre (2004/01/20)
6050 afe 1.243 o shortened offending lines in exch2_send_rx?.template
6051 afe 1.242 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
6052 edhill 1.240 o genmake2: add build & execute test for NetCDF code
6053 afe 1.239 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
6054     old grid files, moved CPP_EEMACROS.h to pkg/exch2
6055 dimitri 1.238 o added useSingleCPUIO flag to monitor.F and mon_out.F
6056 dimitri 1.241 o added temporary hack for sea-ice dynamics on the cube:
6057     metric terms are ignored and it is assumed that
6058     there is no sea-ice on cube faces 1, 2, 4, and 5.
6059 dimitri 1.238
6060 jmc 1.1203 checkpoint52f_post (2004/01/09)
6061 afe 1.236 o added exch2 cube routines to pkg/exch2
6062     o modified hs94.cs-32x32x5 to use it
6063     o added new grid files to hs94.cs-32x32x5
6064 jmc 1.1203 checkpoint52f_pre (2004/01/07)
6065 dimitri 1.228
6066 jmc 1.1203 checkpoint52e_post (2004/01/07)
6067 jmc 1.234 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
6068     for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
6069 jmc 1.235 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
6070     to work with implicit vertical advection and AB ;
6071     o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
6072     o update output (gad_calc_rhs.F changes affect truncation error) of exp:
6073     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
6074 jmc 1.1203 checkpoint52e_pre (2004/01/02)
6075 jmc 1.233
6076     o fix bug in impldiff when Nr=1 or Nr=2.
6077 jmc 1.232 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
6078     o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
6079 jmc 1.229 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
6080     ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
6081 dimitri 1.228 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
6082 dimitri 1.231 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
6083     o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
6084 jmc 1.220
6085 jmc 1.1203 checkpoint52d_post (2003/12/16)
6086 adcroft 1.230 o re-tiled many expts to allow comparison in multi-processor mode
6087     - updated output accordingly
6088     - changed hs94.128x64x5 to use intial T from file rather than use the
6089     random number generator
6090 molod 1.227 o add infrastructure in model routines for fizhi and gridalt packages
6091 jmc 1.220 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
6092 dimitri 1.222 o changes to permit hi-res, cubed-sphere, configuration
6093     - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
6094     - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
6095     - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
6096     of surface winds for the cube
6097     (A verification experiment, based on global_ocean.cs32x15, but with
6098     pkg/seaice turned on and with on-the-fly interpolation from the NCEP
6099     Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
6100     complete with example surface forcing files and matlab scripts to look
6101     at the output and compare it with that of global_ocean.cs32x15.)
6102 jmc 1.223 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
6103     but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
6104     to conform to the common rule.
6105 jmc 1.224 o check-in the first version of the coupler + interfaces for multi-components
6106     set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
6107     - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
6108     - atmosphere: use pkg aim_v23 ; no sea-ice for now.
6109     - ocean and atmos. share the same horizontal grid (no interpolation).
6110     - exchanges between component and coupler is done in forward_step
6111 jmc 1.225 o new verification experiment, cpl_aim+ocn:
6112     coupled ocean - AIM atmosphere on cs32 grid.
6113 jmc 1.217
6114 jmc 1.1203 checkpoint52d_pre (2003/12/06)
6115 jmc 1.217 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
6116 jmc 1.218 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
6117 heimbach 1.213
6118 jmc 1.1203 checkpoint52c_post (2003/11/25)
6119 heimbach 1.213 o Fixing OPTIONS files for use of exf:
6120     - ALLOW_ECCO not needed
6121     - ECCO_CPPOPTIONS.h should not be included from
6122     EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
6123     as has been the case in the past
6124     - All cal/exf related options are currently set in
6125     single header file. Should remain so until we
6126     agree on a consistent new policy.
6127 heimbach 1.214 o Removed all CPP options for cal package.
6128     cal has no more CPP options.
6129 heimbach 1.215 o modified STOREs in GAD_ADVECTION
6130     o corrected key comp. for passkey
6131 heimbach 1.210
6132 jmc 1.1203 checkpoint52b_post (2003/11/23)
6133 jmc 1.212 o new version: "thsice" of thermodynamic sea-ice pkg:
6134     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
6135     - modify fluxes but do not change theta directly;
6136     - light cleaning of bulk_force pkg (still needed with thsice).
6137     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
6138     + output_thsice.txt to test thsice & bulk_force pkgs.
6139     o put back grid & coriolis monitor output.
6140 jmc 1.1203 checkpoint52b_pre (2003/11/23)
6141 jmc 1.211
6142     o call "do_the_model_io" at the beginning (=> dump initial state)
6143     o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
6144 heimbach 1.210 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
6145     (need info on NUMBER_OF_PTRACERS)
6146     o missing PTRACERS headers in some routines
6147     o default tamc.h in pkg/autodiff supposed to crash
6148     to ensure proper customization
6149 dimitri 1.206
6150 jmc 1.1203 checkpoint52a_post (2003/11/17)
6151 jmc 1.208 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
6152 dimitri 1.207 - moved surfaceTendencyTice from pkg/seaice to main code
6153 jmc 1.208 - subroutine FREEZE_SURFACE now limits only surface temperature
6154     and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
6155     => new output.txt for global_ocean.cs32x15 & global_with_exf
6156     - keep the old version of FREEZE for backward compatibility;
6157     global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
6158 heimbach 1.209 - corresponding modifs for TAF directives
6159 dimitri 1.207 o added surface flux output variables to TIMEAVE_STATVARS
6160     o time-averaged output for pkg/ptracers
6161 heimbach 1.209 o fix problem with ECCO-related divided adjoint
6162     snapshot file was missing some ad-variables,
6163     but no warning issued by TAF
6164 dimitri 1.206
6165 jmc 1.1203 checkpoint52a_pre (2003/11/12)
6166 dimitri 1.206 o some bug fixes for #undef REAL4_IS_SLOW
6167 heimbach 1.205
6168     checkpoint52 = ecco_c52_e35
6169     o after testing adjoints of checkpoint51u_post
6170 edhill 1.203
6171 jmc 1.1203 checkpoint51u_post (2003/11/06)
6172 heimbach 1.204 o this is the post-merge tag of the ecco-branch
6173     (needs another clean checkout and re-testing)
6174     o various natl_box_adjoint configs and results
6175     but no input fields
6176     o obcs adjoint not yet merged!
6177     o adding ECCO global 1x1 and 2x2 degree configs
6178     o updated/extended some store directives for seaice
6179     o pkg/ecco now containes ecco-specific part of cost function
6180     o top level routines the_main_loop, forward_step
6181     supersede those in model/src/
6182     previous input data.cost now in data.ecco
6183     (new namelist ecco_cost_nml)
6184     o in ctrl/ cleaned some cross-dependencies and updated CPP options
6185    
6186 jmc 1.1203 checkpoint51t_post (2003/11/04)
6187 heimbach 1.204 o this is the pre-merge tag of the ecco-branch
6188    
6189 jmc 1.1203 checkpoint51s_post (2003/11/04)
6190 edhill 1.203 o cleanup: removed various obsolete #define-s
6191 heimbach 1.204 o pkg/grdchk
6192     - renamed 'ph-grd 3' to 'grad-res'
6193     - merged from ecco-branch
6194     (remaining bug fixes for obcs gradient checks)
6195     - additional high-precision output for testreport
6196     (grep for 'precision_grdchk_result')
6197 edhill 1.202
6198 jmc 1.1203 checkpoint51r_post (2003/11/03)
6199 edhill 1.202 o cleaned up or removed CPP_OPTIONS.h files
6200     o updated results for some of the tests to reflect the new
6201     optfiles (-ieee: -O0 instead of -O3)
6202 heimbach 1.201
6203 jmc 1.1203 checkpoint51q_post (2003/10/30)
6204 heimbach 1.201 o cd_code:
6205     - moved cd_scheme.F -> cd_code_scheme.F
6206     - separate read_checkpoint from cd_code_ini_vars.F
6207     - separated cd_code part from write_checkpoint
6208     - updated AD_SOURCE, generated .flow
6209     - added CD_CODE_VARS.h to the_main_loop
6210     - Moving cd_code specific store dir.s to pkg/cd_code
6211     o ctrl package totally restructured
6212     - pack/unpack now optional and decoupled from
6213     xx_/adxx_ I/O
6214     - ctrl_pack/unpack cleaned
6215     (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
6216     - confined inclusion of AD_CONFIG.h to where necessary.
6217     o genmake2: changed AD dependencies from SRCFILES to AD_FILES
6218 edhill 1.198
6219 jmc 1.1203 checkpoint51p_post (2003/10/30)
6220 edhill 1.198 o create initial cd_code package
6221 edhill 1.199 - WARNING: the initialization of fields within packages
6222     is broken because INI_FIELDS (where READ_CHECKPOINT is
6223     called) is called *before* PACKAGES_INIT_VARIABLES.
6224     This seems to be backwards since
6225     1) its important to initially zero the entire field including
6226     the "halo" region
6227     2) zeroing needs to be done *before* reading pickup info
6228     and the pickup call might or might not happen in any
6229     particular run
6230     - this needs an overhaul for R2
6231 edhill 1.198 o cleanup verification/*/code/GMREDI_OPTIONS.h
6232     o cleanup testreport
6233 heimbach 1.196
6234 jmc 1.1203 checkpoint51o_post (2003/10/27)
6235 heimbach 1.196 o bringing AD-related verif's up to date with genmake2
6236     - carbon/
6237     - global_ocean.90x40x15/
6238     - hs.94.1x64x5/
6239     - (front_relax/ )
6240     o (more) consistent directory structure for AD-related verif.'s
6241     o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
6242     o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
6243     o bug fix in find_alpha.F for MDJWF:
6244     - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
6245     change rho -> rho-rhoConst
6246     - replace call find_rho to find_rhonum
6247     o initialisation of rFlx extended to full array (required by TAF)
6248     and shifted to thermodynamics
6249     o removed PTRACERS.h in ptracers routine
6250     o added surfacetendencyPtr to S/R parameter list pracers_forcing
6251     o Correcting initialisations for fVerU, fVerV.
6252     o helping TAF to recognize dependency on kUp for
6253     fVerU, fVerV
6254     o Replacing delZ by delR in pkg/ctrl/
6255 jmc 1.1203 checkpoint51o_pre (2003/10/24)
6256 dimitri 1.192
6257 edhill 1.195 o undid all of cp51 pending some cleanups and discussion
6258 heimbach 1.197 o added the [#include "AD_CONFIG.h"] statement to all files that need
6259     it for adjoint/tl #defines
6260     o re-worked the build logic in genmake2 to support AD_CONFIG.h
6261     o removed tools/genmake since it no longer works
6262 dimitri 1.194
6263 jmc 1.1203 checkpoint51n_post (2003/10/23)
6264 dimitri 1.194 o modifications to make FREEZE flux visible to pkg/kpp
6265     - moved surfaceTendencyTice from pkg/seaice to main code
6266     - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
6267     - subroutine FREEZE now limits only surface temperature
6268     (this means new output.txt for global_ocean.90x40x15,
6269     global_ocean.cs32x15, and global_with_exf)
6270     o added surface flux output variables to TIMEAVE_STATVARS
6271    
6272 jmc 1.1203 checkpoint51n_pre (2003/10/23)
6273 dimitri 1.192 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
6274 edhill 1.193 o added [#include "AD_CONFIG.h"] to all files that use the following
6275     defines:
6276     - ALLOW_ADJOINT_RUN
6277     - ALLOW_TANGENTLINEAR_RUN
6278     - ALLOW_ECCO_OPTIMIZATION
6279 edhill 1.190
6280 jmc 1.1203 checkpoint51m_post (2003/10/21)
6281 edhill 1.190 o incorporating changes to get TAMC/TAF working in genmake2
6282     - added new TAMC/TAF targets to the Makefile
6283     - various cleanups related to package handling
6284 edhill 1.191 - these changes should have no impact on the forward model
6285 dimitri 1.189
6286 jmc 1.1203 checkpoint51l_post (2003/10/20)
6287 dimitri 1.189 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
6288     - faster algorithm for cal_addtime.F
6289     - higher precision arithmetic, where needed
6290     - pkg/exf *startdate variables changed from calendar date to
6291     model integration time
6292    
6293 jmc 1.1203 checkpoint51l_pre (2003/10/17)
6294 jmc 1.188 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
6295     o enable to apply restoring on S & T only in a latitude band.
6296     o update output (external_forcing_surf modif. change truncation errors)
6297     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
6298 edhill 1.186
6299 jmc 1.1203 checkpoint51k_post (2003/10/16)
6300 jmc 1.187 o change default to: useNHMTerms=.FALSE.
6301     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
6302     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
6303     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
6304     exp1, ideal_2D_oce
6305     - change data file of oceanic exp (leave the results unchanged for now)
6306     exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
6307     o set gravitySign automatically according to the vertical coordinate used
6308     (and change sign: back to "logical" value: +1 when R increases downward)
6309 edhill 1.186 o added an include barrier to the default CPP_OPTIONS.h and
6310     removed the #include "PACKAGES_CONFIG.h" from it
6311 jmc 1.187 o fix a bug in mom_fluxform (from chk51j_post)
6312 heimbach 1.185
6313 jmc 1.1203 checkpoint51j_post (2003/10/10)
6314 heimbach 1.185 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
6315     o adjusted some flow directives (dynamics, thermodynamics)
6316     o added cubed-sphere case to test cost function
6317     o heckpoint_lev?_directives.h now include
6318     pkg-specific directives, whenever those are enabled.
6319     o Moving pkg-specific flow directives to corresponding pkg
6320     Moving pkg-specific differentiation list to corresponding pkg
6321     Moving pkg-specific checkpoint-lev storing to corresponding pkg
6322     ---> conventions are
6323     - pkg_ad.flow
6324     - pkg_ad_diff.list
6325     - pkg_ad_check_lev?_dir.h
6326 stephd 1.181
6327 jmc 1.1203 checkpoint51i_post (2003/10/09)
6328 edhill 1.184 o merge of the branch-genmake2
6329     - knowingly breaks the older genmake
6330     - automatic generation of all ALLOW_${PKG_NAME} defines
6331     - new testreport supersedes older testscript
6332     o large number of package inclusion and header cleanups
6333 jmc 1.1203 checkpoint51i_pre (2003/10/08)
6334 edhill 1.184
6335 edhill 1.183 o new output for adjoin of global ocean vector invariant
6336     o fix for checkpoint of thermodynamic seaice and bulk_force
6337     o Steph gchem various cleanups
6338    
6339 stephd 1.181 checkpoint 51h_pre
6340 edhill 1.183 o fixed some single quotes
6341 stephd 1.181 o modify gchem pkg to be more versatile
6342     o modifications to clean up dic pkg
6343     o add pkg/cfc
6344 heimbach 1.182
6345 jmc 1.1203 checkpoint51g_post (2003/10/02)
6346 heimbach 1.182 o provide links for ARPACK and ADM*TLM
6347     o start removing verification/vero/
6348     o update AD-related stuff
6349     (in particular some IF-statements in model/src/ routines)
6350     o adding to verification/global_ocean.90x40x15/ adjoint of
6351     vector invariant setup
6352 dimitri 1.177
6353 jmc 1.1203 checkpoint51f_post (2003/10/02)
6354 jmc 1.179 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
6355 dimitri 1.178 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
6356 dimitri 1.177 of tracer Green's fucntions for ocean inversion project.
6357 dimitri 1.175
6358 jmc 1.1203 checkpoint51f_pre (2003/08/07)
6359 dimitri 1.175 o Added on-the-fly spatial interpolation capability
6360     "USE_EXF_INTERPOLATION" to pkg/exf.
6361 dimitri 1.176 - This is a temporary Cartesian-grid hack until
6362 dimitri 1.175 the super-duper ESMF coupler becomes available.
6363 dimitri 1.176 - See verification/global_with_exf/README for usage example.
6364     - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
6365     flags and modified pkg/seaice accordingly.
6366 dimitri 1.175 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
6367     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
6368     non-local transport term.
6369 heimbach 1.172
6370 jmc 1.1203 checkpoint51e_post (2003/08/03)
6371 jmc 1.174 o pkg/mom_vecinv:
6372     - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
6373     - add time-ave diagnostic of vorticity advection.
6374     o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
6375     o atmospheric geopotential: - include water vapor effect;
6376     - use p^kappa in p* scaling.
6377 jmc 1.173 o land pkg: read initial state from files.
6378     o AIM : add stratospheric drag in the upper level
6379    
6380 jmc 1.1203 checkpoint51d_post (2003/07/18)
6381 jmc 1.173 o change function ILNBLNK (=> last non-blank char.) to return zero
6382     (instead of the string length) when the string. char is empty
6383 jmc 1.171 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
6384 heimbach 1.172 o modif's to restore TAMC compatibility
6385     - avoid "_d" constructs in PARAMETER declarations
6386     - avoid interrupting lines by comment lines
6387     o Use cluster local disks for purely local I/O
6388     vs. globally visible disks needed for ctrl stuff
6389     (merged from ecco-branch)
6390     - new active_file_loc... and mdsio_..._loc routines
6391     - affected packages: autodiff, ctrl, grdchk, mdsio
6392 heimbach 1.169
6393 jmc 1.1203 checkpoint51c_post (2003/07/08)
6394 heimbach 1.170 o introducing integer flag debugLevel
6395     - debLevZero: suppress all output
6396     - debLevA: standard
6397     - debLevB: equivalent to current debugMode=.TRUE.
6398     o introducing pathname variable mdsioLocalDir for mdsio
6399     that can be specified at runtime
6400     (relevant for cluster I/O to local disk)
6401     `
6402 heimbach 1.169 >>>checkpoint51b_post
6403     adjoint of ptracers
6404     o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
6405     o extended state in checkpoint_lev?, etc.
6406     o alternative ctrl/cost with tr1 or ptracer
6407     o new comlev1_bibj_ptracers
6408     o new ptracers.flow
6409     o made ptracers_forcing same as external_forcing_s
6410     o added verification for adjoint with ptracers
6411     - adm. grdchk fail so far
6412     - tlm. grdchk OK
6413     - checked tapelev/comlev recomputations: OK
6414     <<<checkpoint51b_pre
6415 stephd 1.168
6416 jmc 1.1203 checkpoint51a_post (2003/06/25)
6417 stephd 1.168 o added code for biogeochemistry package
6418     - new pkgs: dic, gchem
6419     - new subroutine in ptracers
6420     o modify code for biogeo packages
6421     - in model/src and pkg/ptracers
6422 heimbach 1.166
6423 jmc 1.1203 checkpoint51 (2003/06/24)
6424 heimbach 1.166 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
6425     - autodiff, ctrl, exf, grdchk, seaice
6426     kept separate packages
6427     - cost, ecco, obcs
6428 heimbach 1.167 o updating verification/internal_wave, verification/lab_sea
6429     (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
6430 heimbach 1.165
6431 jmc 1.1203 checkpoint50i_post (2003/06/23)
6432 heimbach 1.165 o Preparing next differentiable checkpoint and sync
6433     of MAIN vs. ecco-branch
6434     - 1st step: this one is differentiable
6435     - 2nd step: next(! not this) checkpoint will have updated packages
6436     from ecco-branch)
6437 jmc 1.161
6438 jmc 1.1203 checkpoint50h_post (2003/06/20)
6439 jmc 1.163 o new package "land": provide surface BC for AIM.
6440     o pkg/ptracers: apply exchange to all tracers after reading a pickup.
6441 jmc 1.161 o AIM: use true log-P extrapolation for near surface temp (= as in
6442     F.Molteni paper) ; update aim.5l_cs output.
6443 adcroft 1.162 o New variable in PARM03 for more flexible pickups
6444 heimbach 1.164 o somewhat cleaned package initialisation sequence for
6445     ctrl/ cost/ ecco/ in packages_... routines
6446 dimitri 1.160
6447 jmc 1.1203 checkpoint50g_post (2003/05/23)
6448 dimitri 1.160 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
6449     - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
6450     - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
6451     made the default because of faster convergence than ADI
6452 heimbach 1.159
6453 jmc 1.1203 checkpoint50f_post (2003/05/23)
6454 heimbach 1.159 o exf totally restructured
6455     - replaced all exf_set_ routines by one generic exf_set_gen.F
6456     and made sure it's still differentiable
6457     - split exf_getffields.F into new exf_bulkformulae.F
6458     - exf_inscal_/exf_outscal_ suffixes consistent with field names
6459     - updated adjoint/makefile and relevant verif. accordingly
6460 adcroft 1.156
6461 jmc 1.1203 checkpoint50f_pre (2003/05/23)
6462 jmc 1.157 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
6463     + change Evap over land. (update aim.5l_cs output)
6464 adcroft 1.156 o added missing .cvsignores and made uniform across expts
6465     o changed configuration of tidal_basin_2d expt
6466     o added pkg/debug functions for tracing code in fatal crashes
6467     o tidied pkg/monitor to use MONITOR_OPTIONS.h
6468     o new fn in pkg/monitor to stop model if solution grows too big
6469     o removed lots of single quotes from comments
6470    
6471 jmc 1.1203 checkpoint50e_post (2003/05/14)
6472 mlosch 1.155 o make KPP work with PTRACERS
6473     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
6474     nearly a copy of kpp_transport_s
6475     - there is no analogue to SurfaceTendencyS, so I have to use
6476     gPtr(of the surface layer) instead
6477     o add a new platform SunFire+mpi (SunFire 15000) to genmake
6478 jmc 1.1203 checkpoint50e_pre (2003/05/13)
6479 mlosch 1.155
6480 jmc 1.1203 checkpoint50d_post (2003/05/13)
6481 mlosch 1.154 o change kpp output from multiple-record state files to single-record state
6482     files analogous to write_state.F
6483     o reduce the output frequency of cg3d-related stuff to the monitor frequency,
6484     analogous to the cg2d-related output.
6485 mlosch 1.155 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
6486     so that writing to internal file fn (with length 512) fails.
6487 jmc 1.1203 checkpoint50d_pre (2003/05/12)
6488 jmc 1.151
6489 jmc 1.1203 checkpoint50c_post (2003/05/12)
6490 jmc 1.153 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
6491 jmc 1.152 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
6492 jmc 1.151 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
6493     o bug fixed in convective adjustment diagnostic (multi-tile set-up).
6494     o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
6495 dimitri 1.150
6496 jmc 1.1203 checkpoint50c_pre (2003/04/30)
6497 dimitri 1.150 Merging from release1_p13:
6498     o bug fix for pkg/seaice dynamic solver
6499     o Added SEAICE_initialHEFF to pkg/seaice
6500 jmc 1.149
6501 jmc 1.1203 checkpoint50b_post (2003/04/17)
6502 jmc 1.149 o store u*,v* in gU,V instead of in guNm1,gvNm1
6503     o in order to put the momForcing out of the Adams-Bashforth:
6504     move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
6505     to timestep.F
6506     o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
6507     o re-generate output for highly sensitive test-exp:
6508     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
6509 heimbach 1.146
6510 jmc 1.1203 checkpoint50b_pre (2003/04/17)
6511 jmc 1.147 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
6512 heimbach 1.146 o corrected CPP option mismatch in exf_Bulk... functions for case
6513     #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
6514 heimbach 1.145
6515 jmc 1.1203 checkpoint50a_post (2003/03/21)
6516 heimbach 1.145 o Bug fix for merging between c50 and KPP.
6517     ikey was passed from thermodynamics to kpp_calc via
6518     common block rather than being recomputed in kpp_calc,
6519     in contradiction with new key itdkey.
6520     New key ikppkey created, and tamc.h headers updated.
6521 heimbach 1.143
6522 jmc 1.1203 checkpoint50 (2003/03/08)
6523 heimbach 1.144 - 2nd step of merge with ecco-branch:
6524     merge changes in ecco-branch back into main trunk
6525     - bug fix in find_alpha
6526     - more storing in gmredi_calc_tensor.F, kpp_routines.F
6527     - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
6528     - merged some sliced AD support routines
6529    
6530 jmc 1.1203 checkpoint49 (2003/03/06)
6531 heimbach 1.143 merged from ecco-branch:
6532     o exf:
6533     - Enable initialisation of forcing fields to constant
6534     (runtime) values.
6535     - in exf_getffields.F
6536     Reduce i-/j-loop to interior domain, discarding overlaps.
6537     That also fixes wrong TAF-key computations for key_1, key_2
6538     with bulf formulae.
6539     - exf_init.F modify #ifdef for exf_init_evap
6540     - exf_getffieldrec.F, ctrl_getrec.F
6541     The following INT-usages are not safe:
6542     fldsecs = int(fldsecs/fldperiod)*fldperiod
6543     fldcount = int(fldsecs/fldperiod) + 1
6544     and were modified.
6545     o autodiff: checkpoint_lev...
6546     - updated storing for bulk formulae (some arrays were missing)
6547     - added state for seaice package
6548     - synchronized with main branch
6549     o DIVA:
6550     Modif.s in
6551 heimbach 1.144 - the_main_loop.F
6552     - the_model_main.F
6553 heimbach 1.143 and added cost_final_restore.F cost_final_store.F
6554     o With these changes, it is possible to fully separate
6555     the first forward run to compute the cost function (mdthe_main_loop)
6556     and adjoint runs over individual DIVA intervals (adthe_main_loop)
6557     into separate model executions.
6558     This enables better tuning of DIVA to given queue sizes.
6559     o Loss of cost function value in consecutive DIVA runs is
6560     fixed by storing to 'costfinal' file.
6561     o Appropriate call of ctrl_unpack/_pack,grdchk_main at
6562     beginning/end of adjoint integration is accounted for.
6563     The current changes apply to TAF-1.4.26.
6564     TAF has one remaining bug, requiring one manual change
6565     (see MITgcm manual).
6566     o cal: synchronized between MAIN and ecco-branch
6567 heimbach 1.141
6568 jmc 1.1203 checkpoint48i_post (2003/03/05)
6569 heimbach 1.141 o Changes to restore differentiability of code w.r.t. previous tag
6570     (mostly adding new routines to make list and replacing
6571     pressure by totPhiHyd).
6572     o Updated and merged grdchk package
6573     - has both ADM and TLM checks
6574     - works for single- and multi-proc.
6575     - output cleaned
6576     - worked successfully for parallel DIVA
6577     o genmake:
6578     - Adding -platform=SP4
6579     - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
6580     o Modif. for DIVA:
6581     ctrl_unpack should not be called in intermediate DIVA interval.
6582     (similar thing would apply for active files such as
6583     tbar, sbar, psbar, which should not be reinitialised;
6584     only relevant for ecco-branch)
6585 dimitri 1.136
6586 jmc 1.1203 checkpoint48h_post (2003/02/28)
6587 jmc 1.137 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
6588 dimitri 1.136 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
6589     o Added SEAICE_initialHEFF to pkg/seaice
6590 dimitri 1.139 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
6591 jmc 1.135
6592 jmc 1.1203 checkpoint48g_post (2003/02/18)
6593 jmc 1.135 --- EOS:
6594     o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
6595     store total Potential in totPhyHyd for diagnostics & EOS.
6596     o fix restart and overlap Pb when using Z-coord and EOS funct. of P
6597     --- Pressure/geopotential gradient:
6598     o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
6599     o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
6600     ( changes results of global_ocean_pressure )
6601     o NLFS + z-coord.: add eta*Rho' contribution.
6602     o accurate phiHyd when using interface-W at the middle between 2 centers
6603     ( changes results of ideal_2D_oce )
6604     o includes r* 2nd term in potential gradient.
6605 dimitri 1.134
6606 jmc 1.1203 checkpoint48f_post (2003/02/18)
6607 dimitri 1.134 Merging from release1_p12:
6608     o Modifications for using pkg/exf with pkg/seaice
6609     - improved description of the various forcing configurations
6610     - added basic radiation bulk formulae to pkg/exf
6611     - units/sign fix for evap computation in exf_getffields.F
6612     - updated verification/global_with_exf/results/output.txt
6613     o Added pkg/sbo for computing IERS Special Bureau for the Oceans
6614     (SBO) core products, including oceanic mass, center-of-mass,
6615     angular, and bottom pressure (see pkg/sbo/README.sbo).
6616     o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
6617     to avoid negative values in shallow regions.
6618     - updated verification/natl_box/results/output.txt
6619     - updated verification/lab_sea/results/output.txt
6620     o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
6621     o Added useSingleCpuIO option (see PARAMS.h).
6622     o Updated useSingleCpuIO option in mdsio_writefield.F to
6623     work with multi-field files, e.g., for single-file pickup.
6624     o pkg/seaice:
6625     - bug fix in growth.F: QNET for no shortwave case
6626     - added HeffFile for specifying initial sea-ice thickness
6627     - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
6628     o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
6629     kpp_transport_t.F, forward_step.F, and the_main_loop.F
6630     o pkg/seaice:
6631     - adjoint-friendly modifications
6632     - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
6633 jmc 1.131
6634 jmc 1.1203 checkpoint48e_post (2003/02/12)
6635 jmc 1.131 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
6636 jmc 1.132 o dynamics: change definition of computational domain & adapt mom_fluxform
6637     accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
6638     o following exp works with Olx=Oly=2 (and pass through checkbounds option):
6639     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
6640 jmc 1.133 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
6641 jmc 1.132 global_ocean.90x40x15 global_with_exf global_ocean_pressure
6642     inverted_barometer solid-body.cs-32x32x1
6643     (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
6644 jmc 1.130
6645 jmc 1.1203 checkpoint48d_post (2003/02/09)
6646 jmc 1.130 o in preparation for r*:
6647     a) use pre-computed gradient of hydrostatic potential:
6648     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
6649     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
6650     => affects results of glob_oce_pressure (different truncation error)
6651     update output.txt of ideal_2D_oce & global_ocean_pressure
6652 jmc 1.129
6653 jmc 1.1203 checkpoint48d_pre (2003/02/08)
6654 jmc 1.129 o in preparation for r*:
6655     new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
6656     pass the 2 comp. of the grad. as arguments to momentum S/R.
6657     but for the moment, only used if it does not change the results.
6658     o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
6659 jmc 1.126
6660 jmc 1.1203 checkpoint48c_post (2003/02/06)
6661 heimbach 1.128 Modifications in treatment of initial flux forcing controls
6662     to avoid extra storing of flux fields.
6663    
6664 jmc 1.1203 checkpoint48c_pre (2003/01/21)
6665 adcroft 1.127 o Added tidal_basin_2d experiment (currently 1D!)
6666 jmc 1.126 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
6667 jmc 1.124
6668 jmc 1.1203 checkpoint48b_post (2003/01/27)
6669 jmc 1.124 o r* coordinate added in #ifdef NONLIN_FRSURF block.
6670     (modification to pressure gradient not yet implemented)
6671     o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
6672     (for U & V) that are used for vertical advection of momentum.
6673 jmc 1.123
6674 jmc 1.1203 checkpoint48a_post (2003/01/24)
6675 jmc 1.123 o In preparation for r*, use temp. array to compute vertical transport
6676     in flux-form momentum pkg. => change results of few test-exp.
6677     Update output of: exp4, exp5, front_relax, global_ocean_pressure,
6678     lab_sea, natl_box & plume_on_slope
6679 jmc 1.122
6680 jmc 1.1203 checkpoint48 (2003/01/23)
6681 jmc 1.122 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
6682 heimbach 1.121
6683 jmc 1.1203 checkpoint47j_post (2003/01/21)
6684 jmc 1.120 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
6685 heimbach 1.121 o moved adexch from forward_step to addummy_in_stepping
6686     o added exch in ctrl_map_...
6687     o aveFreq.=0. at end of cost_final to avoid overwrite in
6688     reverse checkpointing loop
6689     o Yet more changes in gmredi:
6690     * adgmredi_calc_tensor
6691     avoiding all recomputation of gmredi_slope_limit
6692     * adgmredi_x/y/rtransport
6693     added flag for excessive storing to avoid recomp. of
6694     u/v/rtans, dTdx/y/z
6695     -> this is not really necessary and very memory-consuming
6696     * adgmredi_slope_psi:
6697     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
6698     * gmredi_slope_limit
6699     re-activated full calculation of taperfct for case 'ac02'
6700     o updating verification/ adjoints of carbon, global_ocean.90x40x15
6701 heimbach 1.116
6702 jmc 1.1203 checkpoint47i_post (2003/01/13)
6703 jmc 1.119 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
6704     o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
6705     default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
6706     o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
6707     o gmredi: fix few bugs.
6708    
6709 adcroft 1.118 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
6710 heimbach 1.116 This will be a good checkpoint to plug into the ecco-branch.
6711     o few modif.'s to get latest version adjointed
6712     (mainly kick out code in ini_linear_phisurf)
6713     o modif's to run adjoint with exactConserv
6714     o case GM_BOLUS_ADVEC should be cleaned
6715     S/R gmredi_slope_psi should be cleaned
6716     o verification/carbon now has exactConserv=.TRUE.
6717 jmc 1.114
6718 jmc 1.1203 checkpoint47g_post (2003/01/10)
6719 jmc 1.114 o time-average AIM output: becomes independent from statvars time-average
6720     (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
6721 heimbach 1.115 o After TAF bug fix:
6722     Tested adjoint of gmredi package.
6723     Tests were done with checkpoint47 rather than with latest
6724     checkpoint47f_post since the latter is broken for the adjoint
6725     verification/carbon/ contains both ADM and TLM gradient checks.
6726     Here they are, before they get changed/lost/stolen.
6727     Mostly modif.'s to fix numerical sensitivities.
6728     Gradient checks OK for
6729     - GM_taper_scheme:
6730     * clipping
6731     * ac02
6732     * linear
6733     * glw91
6734     * dm95
6735     * ldd97
6736     - GMREDI_OPTIONS:
6737     * GM_VISBECK_VARIABLE_K
6738     * GM_NON_UNITY_DIAGONAL
6739     * GM_EXTRA_DIAGONAL
6740     * GM_BOLUS_ADVEC
6741     in conjunction with data.gmredi parameters to be checked in
6742     in a few minutes under verification/carbon/code/
6743 cheisey 1.112
6744 jmc 1.1203 checkpoint47f_post (2002/12/28)
6745 dimitri 1.113 Merging from release1_p10:
6746     o modifications for using pkg/exf with pkg/seaice
6747     - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
6748     and SEAICE_EXTERNAL_FLUXES
6749     - pkg/exf CPP options EXF_READ_EVAP and
6750     EXF_NO_BULK_COMPUTATIONS
6751     - usage examples are Experiments 8 and 9 in
6752     verification/lab_sea/README
6753     - verification/lab_sea default experiment now uses
6754     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
6755    
6756 jmc 1.1203 checkpoint47e_post (2002/12/27)
6757 cheisey 1.112 o created a tag prior to creating a branch
6758    
6759 jmc 1.1203 checkpoint47d_post (2002/12/16)
6760 mlosch 1.111 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
6761     at the bottom boundary had an erroneous half slip boundary condition
6762     o added bottom drag and no slip boundary condition capabilities to
6763     oceanic pressure coordinates code
6764     o added new verification experiment global_ocean_pressure, this experiment is
6765     also described in the tutorial section of the manual
6766 jmc 1.1203 checkpoint47d_pre (2002/12/16)
6767 cheisey 1.110
6768 jmc 1.1203 checkpoint47c_post (2002/12/16)
6769 cheisey 1.110 o Added a verification experiment for a global cubed-sphere ocean run
6770     - verification/global_ocean.cubed32x32x30
6771     - uses pkg/therm_seaice and pkg/bulk_forcing
6772 jmc 1.109
6773     o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
6774     o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
6775     when using P-coordinate; only implemented for atmospheric config.
6776     o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
6777     NOTES: requires option NONLIN_FRSURF to be "#define".
6778     o update advect_xz/results/output.txt (left from checkpoint44g_post)
6779 dimitri 1.108
6780 jmc 1.1203 checkpoint47b_post (2002/12/05)
6781 dimitri 1.108 Merging from release1_p9:
6782     o pkg/seaice
6783     - removed GOTO's and added taf directives
6784     - double precision constants to reduce the g77 (Linux)
6785     to F77 (SGI) differences reported in release1_p8
6786     o tools/genmake
6787     - added SGI options
6788     o verification/testscript
6789     - updated to that of checkpoint47a_post
6790     o verification/global_ocean.90x40x15/input/eedata
6791     - modified for SGI f77 compatibility
6792     o verification/lab_sea
6793     - added description of sea-ice model
6794     - added missing matlab routines
6795     - added test of thermodynamics parallelization
6796 jmc 1.105
6797 jmc 1.1203 checkpoint47a_post (2002/11/23)
6798 jmc 1.105 o new pkg: aim_v23
6799     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
6800     for now, keep the same surface forcing as before.
6801     - Part-Cell implemented into AIM; check that Heat & Water are conserved
6802     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
6803     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
6804     o add diagnostic of surface correction term in monitor output
6805 jmc 1.106
6806     o bulk_force and therm_seaice
6807 cheisey 1.107 - Two packages: bulk_force (Bulk forcing)
6808     and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
6809     - Earlier integration from Stephaine Dutkiewicz
6810     and Patrick Heimbach.
6811     - Two ifdef statements for compile time,
6812     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
6813 heimbach 1.104
6814 jmc 1.1203 checkpoint47 (2002/11/15)
6815 heimbach 1.104 differentiable version of checkpoint46n_post
6816     o bug fix in quasihydrostaticterms
6817     o * "clean" adjoint code (in terms of extensive recomputations)
6818     can now be obtained for all GMREDI options (i.e. for
6819     - GM_VISBECK_VARIABLE_K
6820     - GM_NON_UNITY_DIAGONAL
6821     - GM_EXTRA_DIAGONAL
6822     - GM_BOLUS_ADVEC )
6823     * However, wrong gradient check problem remains unsolved.
6824     * New CPP options have been introduced for different
6825     tapering schemes
6826     o external_fields_load now part of differentiation list
6827     o pressure needs multiple storing;
6828     would be nice to have store_pressure at beginning or
6829     end of forward_step, e.g. by having phiHyd global (5-dim.)
6830     (NB: pressure is needed for certain cases in find_rho,
6831     which is also invoked through convective_adjustment).
6832     o recomputations in find_rho for cases
6833     'JMD95'/'UNESCO' or 'MDJWF' are OK.
6834     o #define ATMOSPHERIC_LOADING should be differentiable
6835     o ini_forcing shifted to begining of initialise_varia
6836     o Incorporating QNVS line search routines into MITgcm
6837     (this is separate code, and therefore not under pkg)
6838     lsopt/, optim/
6839     o Updated verification/carbon/
6840     - #define GM_VISBECK_VARIABLE_K
6841     - GM_taper_scheme = 'ldd97'
6842 heimbach 1.103
6843 jmc 1.1203 checkpoint46n_post (2002/11/12)
6844 heimbach 1.103 Merging from release1_p8:
6845     o verification/natl_box:
6846     updating new external_fields_load routine
6847     o New package: pkg/seaice
6848     Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
6849     The sea-ice code is based on Hibler (1979-1980).
6850     Two sea-ice dynamic solvers, ADI and LSR, are included.
6851     In addition to computing prognostic sea-ice variables and diagnosing
6852     the forcing/external data fields that drive the ocean model,
6853     SEAICE_MODEL also sets theta to the freezing point under sea-ice.
6854     The implied surface heat flux is then stored in variable
6855     surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
6856     kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
6857     non-local transport term. Because this call precedes model
6858     thermodynamics, temperature under sea-ice may not be "exactly" at
6859     the freezing point by the time theta is dumped or time-averaged.
6860     N.B.: fairly large differences in accuracy occur across
6861     different platforms/compilers; comparison between
6862     g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
6863     generated output gives:
6864     T S U V
6865     C D M c m s m s m s m s
6866     n p a R g m m e . m m e . m m e . m m e .
6867     f n k u 2 i a a d i a a d i a a d i a a d
6868     g d e n d n x n . n x n . n x n . n x n .
6869    
6870     Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
6871     o GAD:
6872     - generated new common blocks to account for call of
6873     same gad routines with differing traceridentities
6874     (needed to modify tracerIdentity indices in GAD.h)
6875     - generated separate common blocks for case useCubedSphereExchange
6876     (Department of Futurology)
6877     - parameter lists to gmredi_?transport: added tracerIdentity
6878     - added new key indices to tamc.h
6879     o external_fields_load:
6880     - added this routine to TAF list
6881     - needed to make some common blocks global and additional storing
6882     along the same lines as exf package (checkpoint_lev?_directives.h)
6883     o exf:
6884     updated external forcing package
6885     - bug fixes carried over from ecco-branch
6886     (missing OBCS_OPTIONS.h in two routines)
6887     - enable easy to use "no forcing".
6888     - added exf I/O for atmospheric loading
6889     - added exf I/O for runoff data
6890     - transfered scaling between exf <-> MITgcm to exf namelist
6891     o Adding new verification experiment global_with_exf.
6892     This verification experiment is almost identical to the
6893     global_ocean.90x40x15 experiment, except that it uses
6894     the exf (and cal) package instead of the
6895     external_fields_load routine (cf README file).
6896 adcroft 1.94
6897 jmc 1.1203 checkpoint46m_post (2002/11/07)
6898 adcroft 1.101 o modified testscript to return -- when there are no lines of "%MON" output
6899 adcroft 1.100 o added new flag "quasiHydrostatic" for QH mode
6900     and new routine quasihydrostaticterms()
6901 adcroft 1.99 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
6902     New routine: mom_u_coriolis_nh()
6903 adcroft 1.98 o fixed sign of non-hydrostatic metric terms in u and v equations.
6904     Depend on correct sign of gravitySign.
6905 adcroft 1.97 o added work.pc* to .cvsignore in aim directories using ifc
6906 adcroft 1.96 o introduced flag for controllin non-hydrostatic metric terms
6907 adcroft 1.95 o removed gravitySign from PARM04
6908 adcroft 1.94 o switched to g77/ifc from pgf77 in aim experiments
6909 mlosch 1.93
6910 jmc 1.1203 checkpoint46l_post (2002/11/01)
6911 mlosch 1.93 o made convective adjustment work with pressure coordinates:
6912     - changed the direction of k-loop in convective_adjustment.F for the
6913     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
6914     - adjusted the reference pressure k-index in convective_adjustment.F
6915     - adjusted the convection condition in convect.F (in analogy to
6916     calc_ivdc.F)
6917     - convective_adjustment no longer computes anything on the halos
6918     - removed the warnings about negative salinity from find_rho.F and
6919     find_alpha.F; instead the new routine look_for_neg_salinity, called
6920     at the beginning of find_rho, find_alpha, and find_beta, does a
6921     check of the entire slice, if CPP-option
6922     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
6923 jmc 1.1203 checkpoint46l_pre (2002/10/23)
6924 mlosch 1.91
6925 jmc 1.1203 checkpoint46k_post (2002/10/23)
6926 mlosch 1.91 o fixed the verification/global_ocean.90x40x15 experiment:
6927     - new bathymetry (the world according to A., JMC, and M.)
6928     - new initial fields and forcing fields (*.bin files)
6929     - new POLY3.COEFFS (for the next release one should switch to a full
6930     equation of state: JMD95P or MDJWF)
6931     - fixed several errors and redundancies in the data file
6932     - experiment uses looped cells
6933     - added matlab directory with diagnostic scripts for plotting of output
6934 jmc 1.90
6935     o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
6936     - read AIM physics parameters from a file (data.aimphys)
6937     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
6938 jmc 1.89
6939 jmc 1.1203 checkpoint46j_post (2002/10/07)
6940 jmc 1.89 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
6941     o move wVel computation at the end of the time step, in S/R integr_continuity
6942     o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
6943     o update timeave pkg for wVel diagnostic.
6944 jmc 1.1203 checkpoint46j_pre (2002/09/27)
6945 mlosch 1.87
6946 jmc 1.1203 checkpoint46i_post (2002/09/25)
6947 jmc 1.88 o Clean up AIM package (and keep the results unchanged):
6948     include CPP_OPTION and use IMPLICT NONE in all routines ;
6949     declare all the variables _RL ; use _d 0 for all numerical constants.
6950     use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
6951 mlosch 1.87
6952 jmc 1.1203 checkpoint46h_post (2002/09/25)
6953 mlosch 1.87 o cleaned up the use of rhoNil and rhoConst.
6954     - rhoNil should only appear in the LINEAR equation of state, everywhere
6955     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
6956     and the dynamical equations are all divided by rhoConst
6957     o introduced new parameter rhoConstFresh, a reference density of fresh
6958     water, to remove the fresh water flux's dependence on rhoNil. The default
6959     value is 999.8 kg/m^3
6960     o cleanup up external_forcing.F and external_forcing_surf.F
6961     - can now be used by both OCEANIC and OCEANICP
6962 jmc 1.1203 checkpoint46h_pre (2002/09/18)
6963 mlosch 1.87
6964     Added code to convert surface volume flux (fresh water) into
6965     a mass flux when using P coordinates in the ocean (OCEANICP).
6966     Note: It assumes you have set rho0=rhoConst=density of fresh water.
6967 mlosch 1.86
6968 jmc 1.1203 checkpoint46g_post (2002/09/18)
6969 mlosch 1.86 o Include a new diagnostic variable phiHydLow for the ocean model
6970     - in z-coordinates, it is the bottom pressure anomaly
6971     - in p-coordinates, it is the sea surface elevation
6972     - in both cases, these variable have global drift, reflecting the mass
6973     drift in z-coordinates and the volume drift in p-coordinates
6974     - included time averaging for phiHydLow, be aware of the drift!
6975     o depth-dependent computation of Bo_surf for pressure coordinates
6976     in the ocean (buoyancyRelation='OCEANICP')
6977     - requires a new routine (FIND_RHO_SCALAR) to compute density with only
6978     Theta, Salinity, and Pressure in the parameter list. This routine is
6979     presently contained in find_rho.F. This routine does not give the
6980     correct density for 'POLY3', which would be a z-dependent reference
6981     density.
6982     o cleaned up find_rho
6983     - removed obsolete 'eqn' from the parameter list.
6984     o added two new verification experiments: gop and goz
6985     (4x4 degree global ocean, 15 layers in pressure and height coordinates)
6986 jmc 1.1203 checkpoint46g_pre (2002/09/16)
6987 heimbach 1.85
6988 jmc 1.1203 checkpoint46f_post (2002/09/16)
6989 heimbach 1.85 o Enable tangent linear (forward mode) gradient checks:
6990     - extended active file handling to g_... files
6991     - added TANGENT_SIMULATION to theSimulationMode
6992     - extended grdchk package accordingly
6993     o added tangent linear setup in verification/carbon/code_ftl
6994     o added adjoint setup in verification/front_relax/code_ad
6995 mlosch 1.82
6996 jmc 1.1203 checkpoint46e_post (2002/09/05)
6997 mlosch 1.83 o Added new equation of state -> MDJWF
6998     - EOS of McDougall et al., 2002, JAOT, submitted
6999     - caveat: the equation of state is only valid for a smaller (more
7000     realistic?) range of values than JMD95P/Z and UNESCO
7001     - added masks to the calculation of pressure in store_pressure
7002     - added more check values for density in check_eos (ini_eos.F), some of
7003     the old check values are out of the range of the MDJWF-eos, so don't
7004     expect perfect matches for those
7005 jmc 1.1203 checkpoint46e_pre (2002/08/19)
7006 mlosch 1.83
7007 jmc 1.1203 checkpoint46d_post (2002/08/19)
7008 mlosch 1.82 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
7009     'OCEANICP', also initialised field pressure correctly in ini_eos in the
7010     case of pressure coordinates. eosType='JMD95Z' in
7011     combination with buoyancyRelation='OCEANICP' now causes an error.
7012     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
7013     in find_alpha/beta.
7014 jmc 1.1203 checkpoint46d_pre (2002/08/15)
7015 mlosch 1.82
7016     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
7017     so that JMD95Z and JMD95P give approptiate static stability in find_rho.
7018 adcroft 1.81
7019 jmc 1.1203 checkpoint46c_post (2002/08/15)
7020 adcroft 1.81 o Changes necessary for ocean in p-coordinates
7021     - Added new buoyancy relation = 'OCEANICP'
7022     - Added new parameters = gravitySign (this used to be contained inside
7023     the factor dRdZ which I added when we first switched to R coordinates).
7024     X GM/Redi is not compatible (yet)
7025     X bottom drag and no-slip need to be debugged.
7026 jmc 1.1203 checkpoint46c_pre (2002/08/07)
7027 mlosch 1.80
7028 jmc 1.1203 checkpoint46b_post (2002/08/07)
7029 mlosch 1.80 o Added new equation of state -> JMD95Z and JMD95P
7030 mlosch 1.83 - EOS of Jackett and McDougall, 1995, JAOT
7031 mlosch 1.80 - moved all EOS parameters into EOS.h
7032     - new routines ini_eos.F, store_pressure.F
7033     o Added UNESCO EOS, but not recommended because it requires
7034     in-situ temperature (see JMD95)
7035     o Modified formatting for knudsen2.f in utils/knudsen2 and added
7036     unesco.f to be used with POLY3
7037 jmc 1.1203 checkpoint46b_pre (2002/07/31)
7038 mlosch 1.79
7039 jmc 1.1203 checkpoint46a_post (2002/07/31)
7040 mlosch 1.79 o Added (atmospheric) pressure loading
7041     - new field in FFIELDS.h, etc...
7042     - new cpp flag ATMOSPHERIC_LOADING
7043     o Changed hFacC to _hFacC in calc_phi_hyd.F
7044     o Added SHORTWAVE_HEATING to some files for consistency
7045 jmc 1.1203 checkpoint46a_pre (2002/07/13)
7046 heimbach 1.78
7047 jmc 1.1203 checkpoint46 (2002/07/13)
7048 heimbach 1.78 further merges from release1_p5
7049     o new ctrl package
7050     - adopted from ECCO environment to enable optimization
7051     - added Eliassen Palm fluxes to controls
7052     o added Eliassen Palm flux controls to gradient check package
7053     o cost package
7054     - Compatible with new ctrl package
7055     - added Eliassen Palm cost hooks
7056     - modif's of existing cost functions
7057     o Adjoint-related bug fixes in kpp:
7058     - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
7059     - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
7060     o autodiff package
7061     - flow directives:
7062     + new for S/R do_the_model_io
7063     + enhanced for S/R checkpoint
7064     + new gmredi.flow
7065     - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
7066     disable adcommon.h/g_common.h by default.
7067     - fixed problem for adjoint of global_max
7068     o modified verification/carbon/
7069     o New setup for adjoint of global_ocean
7070     o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
7071     o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
7072     o incorporated hooks for sponge layer code (external_forcing.F)
7073    
7074 jmc 1.1203 checkpoint45d_post (2002/07/12)
7075 jmc 1.77 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
7076 jmc 1.76 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
7077     (affects plume_on_slope "cg2d" output)
7078 jmc 1.77 o add new parameter deltaTfreesurf for free-surface time stepping
7079     o exchange gT,gS when using staggerTimeStep & GM & Oly<4
7080 jmc 1.75 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
7081 jmc 1.74 o change phiMin in exp1 (to agree with documentation)
7082     o add new flags:
7083     - T,S forcing inside/outside Adams-Bashforth
7084     - turn off temp,salt advection and/or forcing
7085     - for each tracer, define internal flag for multiDimAdvection & A-B
7086     o monitor: change definition of KE to check conservation of Energy
7087 heimbach 1.73
7088 jmc 1.1203 checkpoint45c_post (2002/05/30)
7089 heimbach 1.73 o Removed f90 comments ("!")
7090     o Modified initialisations to enable exf package for MITgcm
7091     (without invoking ECCO_PACKAGE).
7092     o modifications to gradient check package (Martin Losch)
7093     - enable centered differences
7094     - modified format of standard output
7095 heimbach 1.72
7096 jmc 1.1203 checkpoint45b_post (2002/05/30)
7097 heimbach 1.72 o cleaned exchange calls in cg2d
7098     o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
7099     o included CPP option SINGLE_LAYER_MODE in thermodynamics
7100     to configure barotropic setup (Martin Losch)
7101     o moved some initialisations within bi,bj loop in dynamics
7102     (TAF flow dependency)
7103     o in initialise_varia, moved call packages_init_variables
7104     before convective_adjustment_init
7105     (corresponding adjustment of TAF tape initialisation).
7106     o in calc_diffusivity/calc_viscosity extended domain to full overlap.
7107 jmc 1.70
7108 jmc 1.1203 checkpoint45a_post (2002/05/01)
7109 jmc 1.71 o compute Rho over the whole domain (extend iMin,jMin indices)
7110     o specific exchange for X-slice domain (case Ny=1)
7111 jmc 1.70 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
7112     o solve_for_pressure : set cg2d_x to zero where OBCS are applied
7113 jmc 1.67
7114 heimbach 1.69 checkpoint44h_post = checkpoint45
7115     o Fix to restore differentiability:
7116     place at which packages_init_variables is called in
7117     initialise_varia is crucial for reverse control flow.
7118     o modifications in GMRedi to enable stable adjoint
7119     (corresponding modif's in thermodynamics, dynamics)
7120     o added missing hook for sponge layer code in external_forcing
7121     o modified test cost functions
7122     o storing in gad_advection (plus removal of write(0,*)!
7123     o missing headers TR1.h added in convective_adjustment routines
7124     o errorMessageUnit set non-equal zero in eeboot
7125     (conflict on some platforms, e.g. IBM SP3)
7126     o modified carbon verif.
7127    
7128 jmc 1.1203 checkpoint44h_pre (2002/03/14)
7129 jmc 1.68 o vertical grid option: allow to put the Interface at the middle between
7130     2 cell-centers ; replace delZ in pkg/kpp by drF.
7131 jmc 1.67 o GM Advective form: Tracers are advected using the residual transport (=
7132     Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
7133 jmc 1.66
7134 jmc 1.1203 checkpoint44g_post (2002/03/05)
7135 jmc 1.66 o fix surface correction term in multiDimAdvection (affects plume_on_slope
7136     results) ; ifdef missing in thermodynamics.F
7137 adcroft 1.65
7138     checkpoint44f_pre,checkpoint44f_post
7139     o added PTRACERS package
7140     This allows an arbitrary number of passive tracers to be integrated
7141     forward simultaneously with the dynamicaly model.
7142     + Implemented so far:
7143     - basic forward algorithm (time-stepping, advection, diffusion, convection)
7144     - I/O and checkpointing
7145     - GM/Redi *but* using the GM/Redi coefficient of Salt
7146     + Not implemented so far:
7147     - KPP
7148     - OBCS
7149     + No specific example supplied (yet) but global_ocean.90x40x15 has the
7150     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
7151     line in data.pkg.
7152     + This package is disabled by default since it increases storage.
7153    
7154 jmc 1.60
7155 adcroft 1.64 o testscript: added -cleanup option
7156 jmc 1.63 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
7157     b) enable to filter 2D fields.
7158 adcroft 1.62
7159     checkpoint44e_pre,post
7160     o re-wrote convective adjustment to use pre-calculated weights
7161     Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
7162     Adds: model/src/convective_weights.F, convectively_mixtracer.F
7163     Original calls to convect() still in place.
7164 heimbach 1.61
7165     chkpt44d_pre,post
7166     o added missing EXCLUDE_MONITOR flags
7167     o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
7168     (incompatible typ in MIN/MAX expressions caused problems
7169     on IBM SP3)
7170     o in genmake added variable MAKEDEPEND
7171     plus resetting for case SunOS
7172     o added timer_stats.c routine for IBM SP3
7173     o removed variables in dynamics
7174     !!! I forgot to create tag chkpt44d_pre !!!
7175     !!! But chkpt44d_pre = chkpt44c_post !!!
7176 jmc 1.63
7177     o real fresh water flux implemented with non-linear free-surface.
7178 heimbach 1.58
7179 jmc 1.59 chkpt44c_pre,post
7180     o few fix (mask in shap_s2, EmPmR in external_field_load,
7181     USE_NATURAL_BCS in solve_for_P);
7182     o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
7183    
7184 heimbach 1.58 checkpoint44b_pre/_post
7185     o merge of relevant stuff from the ecco-branch:
7186     - genmake: removed $S64 overwrite for case SunOS
7187     - pkg/exf: update and corrections for field swapping and obcs
7188     - pkg/ecco: parameter lists for the_model_main, the_main_loop
7189     harmonized between ECCO and MITgcm
7190     - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
7191     updated checkpointing_lev... lists for obcs
7192     - model/src: minor changes in forward_step, plot_field
7193     added directive for divided adjoint in the_main_loop
7194     - pkg/mdsio: added mdsio_gl_slice
7195 jmc 1.57
7196     o check parameters & config (chkpt44a_pre,post)
7197 jmc 1.56 o OBC and NonLin_FrSurf.
7198    
7199 jmc 1.1203 checkpoint44 (2002/01/18)
7200 jmc 1.54 o fix bug in mom_vi_del2uv
7201 jmc 1.56 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
7202     o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
7203     o update AIM experiments (NCEP input files)
7204     o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
7205 heimbach 1.55 o added some stuff for AD
7206 adcroft 1.53
7207 jmc 1.1203 checkpoint43 (2001/09/28)
7208 adcroft 1.53 o added two new advection tests
7209     o added global 4x4 degree ocean test
7210     o added test of H&S94 with free surface on cube
7211     o some final mods for gradient check, adjoint,...
7212 heimbach 1.52
7213 jmc 1.1203 checkpoint42 (2001/09/27)
7214 heimbach 1.52 Fixed AD-related problems:
7215     o Store directives up-to-date with re-arranged Adams-Bashforth
7216     (mainly thermodynamics.F)
7217     o New store directives for multi-dim. advection schemes
7218     * new CPP flag ALLOW_MULTI_DIM_ADVECTION
7219     * new common block and key passkey
7220     (mainly gad_advection.F)
7221     o Modified store directives for split of dynamics/thermodynamics
7222     for the case ALLOW_KPP
7223     o Cleaned argument list for timestep_tracer.F
7224 adcroft 1.51
7225 jmc 1.1203 checkpoint41 (2001/09/27)
7226 adcroft 1.51 o re-formatted/added comments in prologues of key subroutines
7227     to work with protex
7228 heimbach 1.47
7229 jmc 1.1203 checkpoint40 (2001/09/27)
7230 adcroft 1.50 o moved calc_gs, calc_gt and calc_tr1 back to model/src
7231     o added FLT (floats) package from Arne along with demo. experiment
7232     o re-arranged Adams-Bashforth scheme for tracers to allow easier
7233     implementation of forward-in-time forcing terms
7234     o more mods for non-linear free-surface including new variable
7235     o modified multi-dim method to work on cube
7236     o bug fix in KPP (from DM)
7237    
7238 jmc 1.1203 checkpoint40pre9 (2001/09/27)
7239 adcroft 1.49 o added DST advection schemes
7240     o fix MPI bug on SGI's
7241     o modifications for non-linear free-surface
7242     o fixed conditionals for fixed flow/passive tracer only mode
7243     o added tension/strain form of stress tensor
7244     o changes to commenting of arguments for TAF/TAMC
7245     o added/updated many matlab scripts
7246 adcroft 1.50 o added multi-dimensional advection method for tracers
7247 adcroft 1.49
7248 jmc 1.1203 checkpoint40pre8 (2001/09/05)
7249 heimbach 1.47 o new package rw/
7250     Added method for dumping intermediate local arrays:
7251     mdsio_writetile - same as mdsio_writefield except works from inside
7252     bi,bj loop
7253     mdsio_writelocal - same as mdsio_writetile except works for local
7254     arrays
7255     write_local_r? - higher-level wrapper for mdsio_writelocal
7256     Controlled by diagFreq. Defaults to zero (ie. no dumps)
7257     Example given at end of mom_vecinv.F that dumps some local arrays.
7258     o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
7259     control flux-form versus vector invariant code.
7260     Switch is runtime flag vectorInvariantMomentum (defaults to false)
7261     or genmake -DISABLE ...
7262     o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
7263     (additional storing is now needed for case vecinv;
7264     currently nothing implemented to switch this storing off
7265     in case fluxform is used since no CPP flag available).
7266 heimbach 1.46
7267 jmc 1.1203 checkpoint40pre7 (2001/08/14)
7268 heimbach 1.46 o bug fix in dynamics.F
7269     calc_viscosity called before k=1,Nr loop.
7270     o added some #ifdef's ALLOW_PASSIVE_TRACER
7271     o cleaned initialisations in ctrl_map_ini
7272     related to TAF
7273 heimbach 1.45
7274 jmc 1.1203 checkpoint40pre6 (2001/08/13)
7275 heimbach 1.45 o split dynamics into thermodynamics & dynamics
7276     o corresponding split of calc_diffusivity into
7277     calc_diffusivity, calc_viscosity
7278     (kpp_calc_diff, kpp_calc_visc).
7279     o Added diffkr, kapgm to control variables
7280     o bug fix in gmredi_slope_limit for ldd97
7281 adcroft 1.44
7282 jmc 1.1203 checkpoint40pre5 (2001/07/31)
7283 adcroft 1.44 o proper initialization of Adams-Bashforth time stepping
7284     + uses forward step for very first step of model (iter=0)
7285     o re-generated *all* output since almost all output is modified by this
7286     change (sorry but we've been putting this one off for about 2 years)
7287     + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
7288     *not* regenerated since they are already out of date and I don't
7289     want to create the impression that they are suddenly working.
7290     o removed KAP stuff for DEC's
7291     o modified/added many .cvsignore files in */code and */input
7292     o added new expt "solid-body.cs-32x32x1"
7293     + this uses an alternative form of ini_curvilinear_grid.F which
7294     is not necessarily any better than the current one...
7295 heimbach 1.43
7296 jmc 1.1203 checkpoint40pre4 (2001/07/30)
7297 heimbach 1.43 o added re-initialisations of utrans,vtrans,rtrans in
7298     calc_common_factors which are crucial for TAF.
7299     o extended iMin,jMin range for calc_common_factors,
7300     calc_diffusivity
7301     o added option ALLOW_PASSIVE_TRACER
7302     o a few minor updates and fixes
7303    
7304 jmc 1.1203 checkpoint40pre3 (2001/07/13)
7305 heimbach 1.42 o created calc_gtr1.F for gad package
7306     o split the_main_loop and re-introduced forward_step
7307     o some recomputations of nIter0 for TAMC
7308    
7309 jmc 1.1203 checkpoint40pre2 (2001/07/13)
7310 heimbach 1.41 o Updated to latest branch of AJA, JMC
7311     o Added gradient check package
7312     o Added routines for passive tracer handling
7313     o Added carbon sequestration sensitivity experiment
7314    
7315 jmc 1.1203 checkpoint39 (2001/05/14)
7316 heimbach 1.39 o Modifications and fixes to support TAMC
7317     (mainly missing or wrong directives)
7318     o Corrected common blocks when fooling TAMC to produce adjoint I/O
7319     in addummy_in_stepping
7320     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
7321     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
7322     o Included following packages:
7323     cal: calendar
7324     exf: external forcing
7325     ecco: essential routines to control use of cal, exf
7326     (NB: this is not the full ECCO environment)
7327 heimbach 1.40 o disabled some packages by default in genmake
7328 heimbach 1.39
7329 jmc 1.1203 checkpoint38 (2001/04/10)
7330 heimbach 1.38 o see notes_c37_adj.txt
7331     o corrected wrong layer index in external_forcing_t
7332     o replaced the_main_loop/forward_step by the_main_loop
7333     o removed forceoutput from write_state
7334     (replaced criteria for initial/final state)
7335     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
7336 jmc 1.36
7337 jmc 1.1203 checkpoint37 (2001/03/13)
7338 jmc 1.37 o mdsio.F routine split and packaged in pkg/mdsio
7339     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
7340     used unless genmake -disable=mdsio)
7341     o allow a more precise surface-geopotential gradient for the atmosphere
7342     taking into account the change in space of Alpha (=1/rho) at the surface.
7343     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
7344     (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
7345     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
7346     Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
7347     [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
7348     o Time-Average diagnostics defined as a pseudo package "timeave".
7349     o pickup files : old pickup (before c35) did not work with new code (c35
7350     and after) unless activating 2 commented lines in initialise-varia.
7351     o Non-Hydrostatic pickup file Pb fixed.
7352     o bug with Rigid-lid version (since c35) fixed.
7353    
7354 jmc 1.1203 checkpoint36 (2001/02/20)
7355 jmc 1.37 o implement Crank-Nickelson barotropic time-stepping
7356 jmc 1.36 o recover Time-Average diagnostics
7357     o fix Pb in checkpoint (PR#19)
7358     o AIM become a standard package ; clean unused CPP_kees
7359 jmc 1.35
7360 jmc 1.1203 checkpoint35 (2001/02/08)
7361 jmc 1.35 o subtantial rewrite of dynamics.f
7362     o allows staggered time-stepping
7363     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
7364     o added bottom drag (linear + quadratic)
7365 heimbach 1.33
7366 jmc 1.1203 checkpoint34 (2001/01/30)
7367 heimbach 1.33 o Modified exchange routines for correct reverse simulation.
7368     o Added verification output to comply with bug fix in impldiff.F
7369     as of c33 (exp2, natl_box).
7370     o Corrected store directives in dynamics.F
7371     o Corrected array boundaries in impldiff.F
7372     o Corrected array dimensions in gmredi.
7373     Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
7374 heimbach 1.34 o Added routine GLOBAL_SUM_INT to global_sum.F
7375 heimbach 1.33 o Added mdsio_gl.F for ECCO purposes.
7376 adcroft 1.32
7377 jmc 1.1203 checkpoint33 (2000/11/30)
7378 adcroft 1.32 o Fixed bug in lower BC in impldiff.F
7379     o Fixed confusion about units of forcing arrays in FFIELDS.h
7380     namely Fu,Fv,Qnet,Qsw,EmPmR:
7381     - Removed verification/natl_box/code/external_fields_scale.F
7382     (did not differ from that in model/src)
7383     - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
7384     (see FFIELDS.h for description)
7385     - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
7386     kpp_calc.F and kpp_transport_t.F
7387     - Removed model/src/external_fields_scale.F and calls to it
7388     - verification/natl_box uses flux data with "atmospheric" sign so
7389     a special version of external_fields_load.F is used to
7390     change the data as it's read in. This way, the arrays
7391     have the right units and signs at all times tha a user could
7392     possibly use them.
7393     o Corrected genmake to delete a temporary file during configuration
7394 heimbach 1.31
7395 jmc 1.1203 checkpoint32 (2000/11/13)
7396 heimbach 1.31 o Scaling of forcing fields moved from external_forcing.F to
7397     external_fields_scale.F, called directly after loading fields.
7398     o Surface relaxation terms added to surface tendency fields in
7399     extra subroutine.
7400     o impldiff.F changed to avoid storing by TAMC of huge intermediate
7401     fields.
7402     o Changes in GMRedi to comply with packaging structure.
7403     o Modifications and bug fixes in KPP package.
7404     o Verification experiment for KPP added (verification/nat_box/)
7405 heimbach 1.30
7406 jmc 1.1203 checkpoint31 (2000/09/11)
7407 heimbach 1.30 o Packages interface brought in line with defined standard
7408     -> new routines packages_...F
7409     -> changes in initialise_fixed.F, initialise_varia.F
7410     -> enables initialisation interface for ECCO package
7411     o Rescaling of external forcing fields immediately after read
7412     (removed from external_forcing.F)
7413     -> new: surface_fields_scale.F
7414     -> affects ini_foorcing.F, external_fields_load.F
7415     o Computation of surface tendencies before tendency updates.
7416     -> new: external_forcing_surf.F
7417     o Change of variable names useGMRedi, useKPP, useECCO
7418     o Further changes in dynamics.F, impldiff.F for TAMC
7419     o Tested for experiments 0, 2, 4.
7420     - not yet tested for GMRedi.
7421     - not yet tested for KPP.
7422 adcroft 1.29
7423 jmc 1.1203 checkpoint30 (2000/07/13)
7424 adcroft 1.29 o Updates for OBCs
7425     o New experiment for test OBCs (internal_wave)
7426     o New output.txt in verification/exp4/results/
7427     o Updates for KPP: calculation of viscosity corrected, new variables
7428     kpp_dumpFreq and kpp_taveFreq
7429     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
7430     and entry for T90 in genmake
7431 adcroft 1.28
7432 jmc 1.1203 checkpoint29 (2000/06/21)
7433 adcroft 1.28 o packaged KPP and GM/Redi
7434 heimbach 1.27
7435 jmc 1.1203 checkpoint28 (2000/06/09)
7436 heimbach 1.27 o Corrected initialization of hFacMin for difference vertical coordinates
7437     o Modified calculation of partial cell thickness to more robust algorithm
7438     o config_summary.F: replaced write_1D_... by write_0D_...
7439     read_write.F: added subroutines write_0D_...
7440     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
7441     included some initialisations required for TAMC.
7442     o routine calc_isoslopes: modified sqrt computation to make it
7443     differentiable for zero argument.
7444     o routines dynamics, impldiff:
7445     included store directives and tape key computations required for TAMC.
7446     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
7447 adcroft 1.26
7448 jmc 1.1203 checkpoint27 (2000/04/10)
7449 adcroft 1.26 o fixed calc_isoslopes() to so that cancellation of terms in tensor
7450     formulation works properly with variable resolution.
7451     o restructured the calling tree between the_model_main() and dynamics()
7452     o split initialise() into initialise_fixed() and initialise_varia()
7453     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
7454     in new routine ini_psurf()
7455 adcroft 1.25
7456 jmc 1.1203 checkpoint26 (2000/04/05)
7457 adcroft 1.25 o moved some #ifdef in optional routines to encompass everything
7458     except the argument declarations. This was using up some memory.
7459     o fixed macros like _ADT to work with both versions of Linux cpp
7460     o cleaned up some unused and uninitialized variables
7461     (helps when debugging with strict compile options)
7462     o split up CPP_EEOPTIONS.h into options and macros
7463     (macros are now in eesupp/inc/CPP_EEMACROS.h)
7464     o patch for 2 processor JAM mode
7465 adcroft 1.24
7466 jmc 1.1203 checkpoint25 (2000/03/15)
7467 adcroft 1.24 o updates for OBCs and NH
7468     o dramatically reduced memory usage
7469     o added "JAM" routines for use on Artic network
7470     o parameterization of convection by implicit vertical diffusion
7471     o added a diagnostic of convective index
7472     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
7473     (this is was partly for OBCs and NH but also in anticipation of
7474     an explicit free-surface option)
7475     o initial state input files for U and V
7476 adcroft 1.23
7477 jmc 1.1203 checkpoint24 (1999/08/02)
7478 adcroft 1.23 o Removed some spurious "REAL"s
7479     o Updated KPP to latest version from JPL
7480     o Added a COS(latitude) in horizontal viscosity
7481 adcroft 1.22
7482 jmc 1.1203 checkpoint23 (1999/05/26)
7483 adcroft 1.22 o Added del^4 diffusion for salt and temperature
7484     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
7485 adcroft 1.21
7486 jmc 1.1203 checkpoint22 (1999/05/18)
7487 adcroft 1.21 o Made many small changes: implicit none, format(i5), etc...
7488     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
7489 adcroft 1.20
7490 jmc 1.1203 checkpoint21 (1999/05/18)
7491 adcroft 1.20 o Introduced new I/O package that supports direct-access records (mdsio.F)
7492     o Split-up mid-level I/O routines
7493     o Updated input data for experiments 0,1,2,4 and 5
7494     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
7495 adcroft 1.18
7496 jmc 1.1203 checkpoint20 (1999/03/22)
7497 adcroft 1.19 o Tidied up open-boundaries some more
7498     o Added non-hydrostatic code
7499     o Fixed some input data
7500     o Modified MPI start-up to work in "coupled" context.
7501    
7502 jmc 1.1203 checkpoint19 (1998/12/15)
7503 adcroft 1.18 o Tidied up directory structure for verification experiments.
7504     o Added new code for open boundaries.
7505     o Corrected advective terms near boundaries.
7506     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
7507     o Implemented free-slip/no-slip BCs and del^4 dissipation.
7508 adcroft 1.19 o Split default parameters out of ini_parms.F into set_defaults.F.
7509 cnh 1.17
7510 jmc 1.1203 checkpoint18 (1998/11/30)
7511 cnh 1.17 o Further changes for optional code generation with
7512     CPP - ugh!
7513 cnh 1.16
7514 jmc 1.1203 checkpoint17 (1998/11/03)
7515 cnh 1.16 o Beginning to incorporating modularity
7516     for supporting atmos. and ocean configs.
7517     o Small changes for TAMC complinace
7518     o New ultra simple test case. Barotropic box
7519     configuration "exp0".
7520 cnh 1.15
7521 jmc 1.1203 checkpoint16 (1998/10/28)
7522 cnh 1.15 o Minor changes to exchange routines to support
7523     accumulation in reverse mode. Adjoint of an
7524     assignment is an addition.
7525     o Changes to support compilation by TAMC (LR(1)
7526     syntax) and by g77 under Linux ( 72 character
7527     limit ).
7528 cnh 1.14
7529 jmc 1.1203 checkpoint15 (1998/09/29)
7530 cnh 1.14 Rewrote exchange routines to allow
7531     o General tile <-> tile connectivity.
7532     o TAMC reverse mode flag ( is this really needed? )
7533     o Variable width overlap and exchange region widths.
7534     o Hooks for sharing data via DMA, Arctic, Memory Channel,
7535     shmput/shmget, VIA, SYSV shmem and every other cool
7536     communication method.
7537 cnh 1.13
7538 jmc 1.1203 checkpoint14 (1998/09/09)
7539 cnh 1.13 Consistent isomorphism chages made. These allow dynamical core
7540     to support both pressure and meters as a vertical coordinate.
7541 cnh 1.12
7542 jmc 1.1203 checkpoint13 (1998/07/17)
7543 cnh 1.12 Release which corrects global_max problem and a couple
7544     of KGM time-averaging diagnostic errors. Also contains
7545     a double-gyre experiment setup as well as the baseline
7546     4 degree global template. The double gyre template is
7547     organised to allow it to be applied automatically to
7548     the baseline configuration.
7549 adcroft 1.11
7550     branch-point-rdot
7551     A few tidy-ups have been made bt the real point of this
7552     check-point (excuse the pun) is to allow a branch to be
7553     made for the purposes of adding the rDot alterations.
7554     I don't want to commit the rDot to the main-trunk until
7555     we've actually tested it...
7556 cnh 1.10
7557 jmc 1.1203 checkpoint12 (1998/07/08)
7558 cnh 1.10 Tidy up and added generic genmake script (formerly
7559     configure script).
7560     Released to testers.
7561 adcroft 1.9
7562 jmc 1.1203 checkpoint11 (1998/07/02)
7563 adcroft 1.9 Re-arranged initialise() and introduced ini_vertical_grid()
7564     and ini_masks_etc().
7565 adcroft 1.8
7566 jmc 1.1203 checkpoint10 (1998/07/01)
7567 adcroft 1.8 Introduced the configure script.
7568     Separated out the diags package.
7569     Added template for writing time-averages of tile/intermediate quantities.
7570     Updated SIZE.h in exp2 and made the data big-endian.
7571 adcroft 1.7
7572 jmc 1.1203 checkpoint9 (1998/06/22)
7573 adcroft 1.7 MPI fix. Filename changes (meta/data). salbin*y stuff.
7574     General tidy-up.
7575     SST.bin SSS.bin added to verification/exp2
7576 adcroft 1.6
7577 jmc 1.1203 checkpoint8 (1998/06/22)
7578 adcroft 1.6 Inludes time-dependant forcing and time-averaging.
7579     Works at 4x4 and 2.8125x2.8125 global
7580    
7581     checkpoint7-4degree-ref
7582     Branch from checkpoint7. Released for application to
7583     global modeling and general modeling - process studies, regional
7584     model etc..
7585     Configured for verification/exp2 - 4 degree global, two process.
7586 cnh 1.5
7587 jmc 1.1203 checkpoint7 (1998/06/15)
7588 cnh 1.5 Created by cnh
7589     Simple 4 degree global simulation
7590     configuration.
7591     Includes climatological wind,
7592     hydrography, bathymetry etc
7593     Does not include Heat Flux and E-P
7594 cnh 1.4
7595 jmc 1.1203 checkpoint6 (1998/06/08)
7596 cnh 1.4 Created by cnh
7597     merged checkpoint5 with CD and
7598     spherical polar code.
7599     Still some problems with GM Redi
7600     abd full topography.
7601 cnh 1.3
7602 jmc 1.1203 checkpoint5 (1998/06/08)
7603 cnh 1.3 Created by AJA
7604     contains updates to GM Redi
7605     and reordered timestepping loop
7606     for Implicit Diffusion.
7607 cnh 1.2
7608 jmc 1.1203 checkpoint4 (1998/05/30)
7609 cnh 1.2 Created by cnh
7610     Contains memory saving macros ( _rdxc etc..) for when
7611     grid variations are limited.
7612     Contains polynomial coeffs for EOS and knudsen program
7613     for generation.
7614    
7615 jmc 1.1203 checkpoint3 (1998/05/26)
7616 cnh 1.1 Created by cnh
7617     Added extra flags for runtime options
7618     Added this file
7619     Added implicit free-surface
7620     Added pre-conditioner
7621     Put compare01 into repository ( compare01/... )
7622     Put data and eedata into repository ( verification/exp1 )
7623    
7624     checkpoint2
7625     Created by AJA
7626     Added GM/Redi
7627    
7628     checkpoint1
7629     Created by AJA
7630     Restructured kloop in dynamics.F
7631     Added non-linear EOS
7632    
7633 cnh 1.2 baseline
7634     Original checked in code
7635 cnh 1.1

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